Molecular Model.Chem. Info
Molecular Model.Chem. Info CHEM 2101
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Computational Chemistry 81109 1 COMPUTA TIONAL CHEMISTRY AND MOLECULAR MODELING CHAPTER ONE CHEMICAL APPLICATIONS OF COMPUTERS 1 INTRODUCTION Chemists were among the earliest professional people to recognize that computers could revolutionize their activities Many of the early uses of computers simply involved speeding up the labor intensive calculations that were previously performed using slide rules electro mechanical desktop calculating machines and IBM punched card devices Today it is possible to accomplish in a few minutes what would have taken a pre 1950s scientist several lifetimes to accomplish The rst generations of mainframe computers were strictly number in number out machines By today s standards these were dinosaurs that took up a lot of space had miniscule brains and worked at a tortoise like plod Replacing the vacuum tubes by semi conducting devices opened up the possibilities for miniaturization of the hardware and acceleration ofthe tasks Gradually the picture of a computer being no more than a number cruncher has faded and has been replaced by a multi faceted information processor That evolution has provided the chemist with a steadily increasingly range of activities that can be performed more rapidly and ef ciently than ever before Despite the many revolutionary changes that have occurred in computer design and function over the past half century there are many aspects to computer architecture that have remained unchanged Computational Chemistry 81109 2 2 THE ANA TOMY OF A COMPUTER We can identify four major body parts of a computer 1 2 3 4 21 The central processing unit CPU that serves as the heart of the computer and to a biochemist might be thought of also serving the role ofthe liver The memorythat can be thought of as being the brain ofthe computer The input devices that serve the functions of the eyes and ears of the computer The output devices that at a pinch might be thought of serving a role that is similar to that of a mouth The Central processing unit CPU The central processing unit is a programmable electrical circuit that is used to transfer information from one internal or peripheral location of the computer to another It might be compared to a railroad marshalling yard The locations include input and output devices together with the various types of memory where information is stored and the bank of registers where the actual processing such as the arithmetic operations takes place The information is encoded in a binary format The simplest element bit of code is either a 1 or a zero That corresponds to whether or not a speci c memory location has been magnetized Eight bits of code form a byte Computational Chemistry 81109 3 22 The performance level of a CPU is advertised in terms of the number of bits that can be transferred simultaneously in one cycle and the number of such cycles that can be performed per second is called 32 bit architecture meaning that information is moved around in 32 bit four byte Most current desktop computers have what packets Workstations are likely to have 64 bit architecture Microsoft Vista is available in either a 32 bit or a 64 bit version The typical clock speeds of new desktop computers and workstations as measured in Hertz cycles per second have increased enormously in the past decade For many years the motivation for faster computer operation was better number crunching That is still an important consideration for theoretical chemists and physicists In the summer of 2009 manufacturers were promoting desktops with 30 GHz processors and Laptops in the 2 3 GHz range 1 GHz is equal to 109 cycles per sec There is another ingredient of fairly recent origin and that is the need for rapid changes in the graphical images that are generated on the screens of computer monitors Fortunately for the scientists there is an economic driving force from those members ofthe general public who indulge in computer games of death touchdowns and destruction Memory In order for a computer to perform its tasks it has to be provided with programs instruction sets and data information When a computer is turned on it accesses a small permanent memory bank that is kept intact by means of a battery This permanent memory keeps track ofthe date and time It also contains the BIOS Basic Information Operating System The BIOS searches among the available storage devices for a program Computational Chemistry 81109 4 23 called AUTOEXECBAT that sets the computer in motion One can change the settings of BIOS by means ofthe function keys The instruction sets that are necessary for the operating system of the computer to perform its various tasks are transferred from their permanent storage locations such as the hard disk to the computer s own random access memory RAM RAM is volatile meaning that it disappears when the computer is shut down While a program is running information is being rapidly moved between the storage sites warehouse in memory and the registers workbench where the processing takes place As programs have become more sophisticated so the demands upon available memory have increased in spectacular fashion 1024 megabytes is now common for new personal computers with the option of expanding the memory to 4 gigabytes Input devices 231 Magnetic Storage Devices For the majority of personal computer applications the programs and data are stored on a magnetic hard disk As the variety and sizes of computer programs has expanded so has the need for more and more permanent storage space Hard disks with a capacity of 200 gigabytes are now common It is possible to augment the capacity of internal hard disk with a portable external hard disk Computational Chemistry 81109 5 Earlier personal computers were equipped with a 35 inch oppy disk drive The so called floppy disk represents a very useful means oftransferring modest amounts less than 144 Mbytes of information from one computer to another The 144 MB capacity disks are labeled as HD High Density One may still run across 35 inch disks which are labeled DD Double Density which only hold 720 KB of information Most of the student accessible Desktop computers include a oppy disk drive 525 inch oppy disks which were actually quite oppy are pretty much a thing of the past This happens to be the same size and CDs and DVDs The last few years have seen the introduction of high capacity removable disks Zip disks are capable of storing 100 or 250 MB of programs and data The disks themselves are slightly larger than the 35 floppies but still small enough to fit in a shirt purse orjacket pocket The Zip drives can be also be portable and linked by cable into the USB or printer ports of desktop and laptop computers They can alternatively be internal and as such a permanent part of the host computer The drives are relatively inexpensive 100 but the disks are currently about 10 each External Hard Disks of the order of 20 100 gigabytes are relatively inexpensive At least one model can be programmed to backup selected files automatically The oppy disk has been largely replaced by small portable devices that plug into USB ports and have capacities ranging from 500 megabytes to 16 gigabytes Flash cards are also available for storing digital images Computational Chemistry 81109 6 23 2 233 Compact Disks Most commercial software at this time comes burned on to compact disks CDs That has led to the situation where virtually all ofthe new computers have at least a CDDVD player as a component The players themselves are very similar to those in audio systems In fact one can play music at the same time as one is doing more conventional computer work Individual CD players ROMs are rated in terms of the speed at which coded data as opposed to music can be transferred on to the hard drive of the computer The rating 24X means that it operates at 24 times the original standard speed Unlike the hard disks and oppies which store encoded information magnetically compact disks are optically encoded and the information is transported by means of reflected laser light DVD technology is gradually replacing CDs because of the increased storage potential Magnetic Tapes Programs and data were at one time almost exclusively stored on magnetic tapes The tapes for a desk top computer were about the same size as a music cassette tape Mainframe computers used tapes that were typically about two feet in diameter For everyday use tapes have the distinct disadvantage of being one dimensional needing to be unwound to locate a single piece of information while with a disk two dimensional the location of an item of information is speci ed by both the track number and its place on that track Computational Chemistry 81109 7 On the other hand magnetic tapes tend to be more robust and accident free than disks For that reason it is advisable to maintain on a tape a recent back up version ofthe important information that is on the computer s hard disk High capacity external harddisks are also being used for backup purposes 234 Keyboards 2 I am entering these words into my computer using a keyboard A typical keyboard which is used in conjunction with a desk top computer has several basic components The largest area of a computer keyboard is virtually identical to a typewriter keyboard The letters of the alphabet are arranged in exactly the same order The typewriters and computers used in English speaking countries have the QWERTY keyboard In France the keyboard is of the AZERTY variety The distinction occurs in the rst row of letters The numbers 1 O are on the top row There is a shift key a space bar and a Caps Lock key for switching to upper case letters just as there are on most typewriters There is also a Tab key a Backspace key and a carriage return Enter There are two other keys in the main part ofthe computer s keyboard that do not appear on a typewriter One of these is the Control Key CTRL The other is the Alternate Key ALT These keys can be used together with one or more letter keys to initiate short cuts in different programs For example if I enter the number 130 while I am holding down the alternate key I produce the French letter Computational Chemistry 81109 8 3 4 5 6 Somewhere on the keyboard you find a set of keys that are labeled F1 F12 These are called function keys and serve different purposes in different programs Typically the function keys initiate a sequence of commands Desktops but not most laptops have a separate numeric keypad The digits 1 O are set out much like those on a telephone or a TV remote Also on that keypad are keys for performing the four arithmetic operations There is a Num Lock key that is used to activate the keypad If it is not activated many of the keys revert to being a duplicate set of editing keys There are ten editing keys When we are editing a document or a table of numbers we need to be able to move to the offending letter or word Our place is marked by a cursor My cursor is a flashing vertical line that moves along the row as type I can move the cursor up or down left or right by using the appropriate arrow keys or by using the mouse If I wish to make larger moves there are page up and page down keys Pressing the Home key takes me to the start of the row and the End key to the end Control Home takes you all the way to the start of the document while Control End takes you to the very last word Letters or words can be highlighted using the mouse and then banished using the Delete key The Insert key is a toggle in start up mode words typed in the middle of a document will automatically be inserted with the existing text being pushed backwards Pressing the key switches to typing over existing text Moving around the text is made easier by using a pointing device instead of the editing keys The most common pointing device is the Mouse Laptop computers come with a variety of pointing devices l have personally used a Roller Ball an Accupoint pencil eraser and a Touchpad Handheld palmtop computers use styluses Computational Chemistry 81109 9 Pressing down on the left button on pointing devices can be used to highlight sections oftext or spreadsheets that one wishes to copy or delete 235 IN TERFACING Scanners There is a large variety of scanning devices that can send digitally encoded images to a computer One of the simplest is the bar code reader at the check out counter ofa grocery store Printed and photographic material can be optically scanned and the image encoded When text is involved the computer may be helped in its task by an Optical Character Recognition OCR program Some of the newer printers can convert a scanned text file into a Microsoft Word document Voice recognition and interpretation programs are available but it is not evident that they are being widely used by the general public They are used for the TV closed captions by the media often with amusing results Meters There are many probes and sensors like thermistors and light meters that generate an electric current Traditionally that current was used to cause a de ection of the pointer on a meter Such currents can be digitalized The digital value can be shown on an LCD display or it can be transported through an interface card to a computer This kind of procedure makes it possible for chemical instruments to be operated from a computer keyboard The instructions being transmitted to the instrument can be modi ed in response to the information being provided by the sensors Computational Chemistry 81109 10 235 CHEMISTRY ON LINE Local Area Networks There are situations in which it is desirable for several computers to share information One mundane situation would be that of a department store where each check out clerk needs to have access to a common inventory and price list The information is maintained in the memory of a central computer that is frequently referred to as the server Each clerk has access to a terminal slave that may have very limited capabilities dumb or may be able to perform a fairly wide range of independent functions smart The cluster of server and slaves makes up a local area network The slaves will be able to communicate with the server and possibly with each other The information will be passed along cables or by radio wireless transmission The server of a local area network may be able to communicate with other networks using telephone or wireless connections Large corporations are likely to have local networks at several different locations These local networks are linked together to form a kind of super network Firewalls can be set up to avoid rival corporations from accessing proprietary information Global Networks Most academic chemists are not deeply concerned with security They are very much concerned however with the exchange of ideas and with having rapid access to vast pools of information Computational Chemistry 81109 11 It is possible using telephone or broadband cable communications to link together computers in every part of the planet The global communications network is what is called the Internet Access to the Internet from your school home or place of work is provided by an Internet Service Provider ISP We at UTEP have our own ISP The address is utepedu The letters edu identify the ISP as being operated by an academic institution The most widely used ISP is America on Line AOL whose address is aolcom com is short for commercial Many commercial enterprises have their own lSPs An important ISP for chemists is acsorg In order to link up with your ISP you need to have been given a username account name For example my username is mdavisutepedu You will also need to have a password that is recognized by the ISP but known only to yourself hopefully The user name may or may not be the same as your email address mine is There are two main personal uses for the Internet E mail has transformed communications to a remarkable extent Whereas it took about three weeks for a scientist in the United States using snail mail to exchange letters with a colleague in Europe e messages can be exchanged within a matter of hours Manuscripts complete with tables and graphs can be sent as attachments to e messages That means that they can be sent from one computer to another The World V de Web www is a bountiful source of information To move from one ofthe millions of sites to another one makes use ofa program that is called a Browser The most familiar browser is Internet Explorer Computational Chemistry 81109 12 24 Once having accessed the browser one starts the hunt for speci c items of information There are several programs that can seek out web sites that have information about a topic that you have indicates by means of a keyword or a set of keywords The programs are called Search Engines Google and Yahoo are two ofthe most widely used search engines Output Devices There isn t much point in processing information and leaving the result in the memory ofyour computer only to have it evaporate when you pull the plug 241 The Monitor The monitor allows you to keep track of what is going on as you use your computer lam able to see the results of my typing as work on this document In common with every other type of computer hardware the monitors have become progressively larger in terms of screen size and fancier over the years The bulky CRT monitors have almost completely been replaced by atscreen LCDs 242 Magnetic and Optical Storage Devices Just about all of the magnetic disks and tapes that were mentioned as input devices can also be used as output devices Floppy Zip and ash disks can be used for transferring information from one computer to another as well as for storing programs and documents While Compact Disks were originally standard fare as input devices it is only more recently that they have come to be used to store the output of a computer It is possible and becoming more popular to burn one s les onto a compact disk using the right kind of CD player read write While DVDs are mostly used to store movies they are becoming increasingly employed for storing personal data and music les Computational Chemistry 81109 13 In addition there are a variety of devices like MP3 players available for downloading music from the Internet or compact discs 243 Via an Interface It is possible to control the operations of scienti c instruments and numerous types of machinery by sending instructions from a computer keyboard Most of the modern major chemical instruments include a computer as an integral interfaced component 244 Via the Internet We can disseminate information in a variety of ways using the Internet E mail is one obvious possibility We can also create a web page or pages with information that others can easily access Computers can also be used as paperless FAX transmitters 245 Hard Copies The printed page is still a very useful way of storing and distributing information The original electronic printers were of the dot matrix variety They were in vogue long enough that there must be millions of them still in good shape being stored around the world Modern printers come in two major varieties Laser jet and Ink jet The names refer to the technologies that they use Laser printers tend to be more expensive to buy but they are faster and more economical to run There is still a substantial but rapidly decreasing difference in cost between those laser Computational Chemistry 81109 14 printers that print in black and white and those capable of color printing lnk jets or Desk jets are cheaper slower and more expensive to operate 243 Audio systems Most computers that can be purchased in the commercial market place have sound systems These can be as primitive or as fancy as one wishes Music CDs can be played in the background while you are involved in the more conventional computer operations Computer games have sound effects as do many other types of programs SOFTWARE OPERA TING SYSTEMS For any task that we wish a computer to perform we need to create an instruction set The instructions that we give need to be translated into a language that the computer can understand Since the CPU is only capable of performing one very rudimentary operation at a time the machine language has to be very simple A relatively straightfonNard operation like multiplying two numbers together is likely to require a substantial number of machine language instructions There are a limited number of machine language instructions We might think of these instructions as being like the letters of an alphabet From the alphabet we can construct words The words represent sequences of basic instructions The dictionary of words de nes the assembly language The same central processing unit may be controlled by several different assembly languages The assembly language is a key part what is called the Computational Chemistry 81109 15 operating system The operating system controls all of the computer s peripheral hardware as well as the functions of the central processing unit Keyboard instructions can be given to the operating system using a job control language JCL Some job control languages are relatively simple to learn because the commands are words or abbreviations that are easily remembered Other control languages are cryptic and thus dif cult to learn and easy to forget IBM PCs clones almost exclusively used the Microsoft Disk Operating System MS DOS MS D08 is one ofthe simpler operating systems to use but it requires memorizing some of its job control language That difficulty which presented an obstacle to many would be computer users was circumvented by putting a graphical user interface GUI between the operating system and the user The GUI for MS D08 is Windows Icons symbols and menu items have replaced the commands which were previously entered from the keyboard The desired activities are initiated by means of the mouse or the Enter key MS D08 is no longer a separate system but a component ofV ndows The versions of Windows that preceded XP were capable of running programs that were written explicitly for MSDOS In early 2007 Microsoft introduce the Vista family of operating systems One nice thing about the higher level versions of XP and Vista is the possibility of creating one or more virtual machines This provides the means for reserving a part ofthe computer s RAM and hard disk memory for employing earlier operating systems Windows 98 and ME and software applications that are not supported by XP or Vista IBM created its own operating system OS2 which was quite popular at one time The Macintosh computers manufactured by Apple have their own operating system and GUI packaged as a single item Computational Chemistry 81109 16 Most of the heavy duty work stations like those manufactured by Silicon Graphics SGI and Sun Microsystems use UNIX operating systems While the Unix systems have graphical interfaces they still place some reliance on their rather cryptic job control language A relatively new operating system called LINUX that claims to be transportable between different computing environments has gained popularity but not a substantial market share PROGRAMMING LANGUAGES Some computer tasks call for the use of custom written programs For many other tasks there exist several appropriate packages of programs that are available from commercial sources This is sometimes referred to as canned software There are several languages that can be used for writing home made programs Originally there were two dominant programming languages 00 is a business oriented language which has never been of much interest to chemists Scientists and engineers adopted the formula translating language called FORTRAN There are still people writing their own programs in Fortran There are also some commercial programs that have been coded in Fortran The early desktop computers lacked the memory to accommodate the Fortran translation code A fairly simple analog of Fortran was invented That language was called BASIC The program code that we write has to be translated into a code that the operating system can comprehend and work with The preferred way of doing business is to translate all of the program code before running into assembly language This process is known as compilation Programs using the rst versions of BASIC were not compiled but interpreted one line of code at a time Computational Chemistry 81109 33 17 BASIC has gone through several stages of evolution Graphic capability was added in GWBASIC Gee Whiz Substantial improvements in performance were made available in QBASIC Quick The most recent change has been to a version that has a graphical interface providing menus and icons That is called Visual Basic This is one of the languages used by commercial software producers A version of Visual Basic is embedded in Microsoft Excel and Microsoft Word A different type of programming languages known as structured languages came into vogue about thirty years ago The ground breaker was called PASCAL In time C has replaced PASCAL The C language has evolved along much the same lines as BASIC Visual C is the counterpart to Visual Basic Those two languages appear to be the dominant forces in the programming market The Internet calls for programming special instructions Java is a language that has been created for the speci c purpose of producing web pages There are other languages out there which have their adherents CANNED SOFTWARE There is an extensive range of computer tasks for which factory made programs are readily available We shall limit ourselves to the types of programs that might be used by a scientist at the work place I might note that in my travels I have gained the impression that the most widely used program in scientific laboratories is actually the game of Solitaire which comes with V ndows In its defense it is claimed that playing Solitaire is a good way of improving one s dexterity in handling a mouse Computational Chemistry 81109 18 331 MICROSOFT OFFICE AND SIMILAR PACKAGES Microsoft Of ce is a set of programs each of which serves a speci c purpose which has been written to work together We shall be taking a closer look at some of the individual programs later For the time being we shall simply identify their functions Students and faculty should be aware of the opportunity through the university bookstore to purchase Microsoft Of ce as well as V ndows XP at very reasonable prices Microsoft Word and Word Perfect These appear to be the two best selling word processing programs There are others some of which have been specially designed for use by scientists and engineers They are used for creating documents I am using one ofthe more recent versions of Microsoft Word to create this document Word processing programs have gone through numerous evolutionary stages The earliest versions of both Microsoft Word and Word Perfect for IBM PCs ran under MS DOS In that environment the various commands for editing saving and printing documents were cumbersome The more recent versions run in either a Windows or a Mac environment The commands are initiated using menus and icons A document that is created in Word is saved as a File The le must be assigned a name At one time the name could not be longer than 8 letters but that restriction has been removed This le is actually called COMP1docquot The three letter extension doc identi es it as a Word le Files created and retrieved by different programs have different extensions If the le is to be stored on the computer s hard disk or one of the high capacity portable disks it is smart to keep it together with related les in a speci c Folder This le is currently being kept in a folder called 2101quot which Computational Chemistry 81109 19 is in turn a subfolder of website on my hard disk Some people like to build an elaborate hierarchy of Folders and Subfolders To complete the address location of a le we need to specify what storage device it calls home The pre x C the colon is an important component for the address usually indicates the Computer s hard disk Some people like to partition their hard disk into several virtual disks each of which is assigned its own letter symbol It is also possible to install more than one hard disk on the same computer The pre x A usually represents the 35inch oppy disk drive The IBM PCs have retained a feature of the earlier versions of MSDOS which dictates that they look for the program that loads the operating system on Drive A However that is not where the start up program is normally kept except for emergency situations As a consequence if you have accidentally left a disk sitting in the A drive you will get an error message It is possible to insert tables pictures and graphs into a word processed document Computational Chemistry 81109 20 Microsoft Excel Lotus123 and QuattroPro These are the names of three of the most widely used spreadsheet programs Excel has by far the lion s share of the market A spreadsheet has the appearance of a large rectangular matrix The columns are labeled with letters and the rows with numbers The individual elements of the matrix are called cells The cell address V4 is in the Vth 22 column and the 4th row The cells contain either numeric or alphanumeric data They may also contain formulas If cell W2 contains the formula SUMBZV2quot itl will contain the value obtained by summing the numerical contents of the cells ranging from B2 to V2 Formulas can easily be copied from one cell to a range column or row of cells That makes it possible to manipulate large amounts of data simultaneously Spreadsheet programs provide the capability for generating plots of one s data complete with axis labeling and legends for different sets plotted on the same axes Computational Chemistry 81109 21 Spreadsheet programs also offer some curve tting capability For more sophisticated data analyses one can export a spreadsheet or part of a spreadsheet to one of the higherlevel statistical programs It is possible to write visual basic macros These are programs that are accessible in Excel which can manipulate Excel le data Database Software A computer database is similar to a set of index cards Typical uses are mailing lists and inventories A database program would also be a suitable vehicle for creating a list of references to journal articles and books ln constructing a database one must decide upon a number of categories of information Typical categories for creating a reference collection would be 1 Title 2 Authors 3 Journal 4 Year 5 Volume number and page 6 General area 7 Types of content primary data tables new theory experimental innovation etc One can sort the records by any one ofthe categories of information It does not seem to be as common as it was for the major of ce software packages to include a data base program Some versions of Microsoft Of ce include Access The very handy Microsoft Works package which is a scaled down counterpart to Of ce has a useful data base program Computational Chemistry 81109 22 Microsoft Works For the user who does not require very sophisticated software the package called Microsoft Works is a good investment It consists of a word processing program a spreadsheet program and a data base program It is possible to transfer les from these programs to the more sophisticated Microsoft Of ce versions In earlier editions the word processor was a special version for Works but recent versions include Microsoft Word Microsoft Works also comes with communications software Microsoft Powerpoint This popular program is used for creating slides and transparencies for various kinds of presentations including chemistry seminars The slides can be stored on a computer s hard disk a ash disk or a oppy and projected on to a screen All of the foregoing software packages have been created to be used by the general public It is almost essential for any professional person to be able to use a word processor Scientists engineers and business people are expected to know how to put together a spreadsheet Many businesses and organizations have special database software written for them Microsoft Frontpage For those who want to construct their own webpages it is possible to convert documents that have been created in Microsoft Word into either the html hypertext format or the pdf format Then using a FTP le transfer protocol one can move these les to the webpage Computational Chemistry 81109 23 Adobe Acrobat While converting word documents to thehtm format can be handled in the Microsoft Word program creating pdf les requires installation of Adobe Acrobat on your computer Acrobat reader is provided as a free download by Adobecom There is a great deal of software on the market which is of no interest to us as potential scientists and engineers There is however a lot of software that caters to the special interests of chemists and of scientists and engineers in general That is what this course is largely about 332 SOFTWARE for CHEMISTS We start out by distinguishing between learning software and doing software Most if not all ofthe latest generation of general chemistry textbooks come with a companion CD Some of these are a little corny others have quite substantial merit There are also some generic learning programs either on a CD or a set of floppies Some of the learning software can be stored on the hard disk of a network server and accessed from a number of terminals simultaneously Some of the publishing houses have interactive websites that use computer animation as a learning tool Some of the more advanced chemistry textbooks are also packaged with compact disks There is also generic software for learning the rudiments of organic chemistry Doing Chemistry Software The following pages contain a list oftopics that can be more easily learned through the power of computer graphics Computational Chemistry 81109 24 1 Molecular Geometry In order to understand the nature of chemical reactivity it is very helpful to be able to visualize the structures of molecules There are several ingredients in the visualization process 1a Atomic orbitals and hybridization The arrangement of the covalent bonds that radiate out from a single central atom is determined by the nature of the valence shell atomic orbitals that are used by that atom We can make use of software that helps us to appreciate the shapes of both the pure s p and d orbitals and the various hybrids that can be formed from them 1b Single center structures ABn containing lone pairs and single bonds For each hybridization scheme the hybrid orbitals may be used to form single covalent 6 bonds or accommodate lone pairs of electrons The shapes of the molecules that are involved can be learned and appreciated by looking at computer generated images that can be rotated in a manner that gives a three dimensional mental image 1c Single center structures containing multiple bonds Multiple bonds are generally envisaged as being comprised of a sigma 6 bond and one or two pi 11 bonds The more commonly encountered pi bonds are formed from pure p atomic orbitals Pi bonds may also be formed from the combination ofa Computational Chemistry 81109 25 p and a d atomic orbitals or from two d orbitals There is also the possibility of two d orbitals combining to form a delta 8 bond All of the multiple bonding situations can be appreciated more easily from studying computer generated images than from sketches on a blackboard or pictures in a book 1d Orbital overlap and molecular orbitals Bond formation by electrons in atomic orbitals can be nicely shown by using sequences of computer generated images These images can be used as a means of comparing the valence bond and molecular orbital approaches to describing covalent bond formation 1e Delocalized bonding Computer generated images can help to improve our understanding of both resonance theory and multi center molecular orbitals 1f Complex formation by transition elements We can use computers to generate images that demonstrate the way in which we envisage that ligands bind to transition element ions and atoms to form complexes This can also provide a vehicle for introducing crystal field and ligand eld theories Computational Chemistry 81109 26 1g Conformational isomerism The rst step in discussing structures more elaborate than those with a single central atom is to consider the different structures that can be generated by an internal rotation around a single covalent bond That introduces the marked preference for staggered over eclipsed structures and the distinction between trans and gauche conformers 1h Geometric isomerism Here we shall discuss different molecules that have the same connectivities Cis and trans isomers of 2 butene are one obvious example We shall aslso consider geometric isomers of complex ions such as the cis and trans versions of the PtCl4239 ion 1i Optical isomerism Computers are particularly useful for illustrating the differences between optical isomers 1 Structural isomerism Many of the learning software packages identify the simpler forms of structural isomerism and the various nomenclature schemes for distinguishing between them 2 Molecular Energy Simple molecular mechanics MM programs like PCModel or the MMX subprograms in Spartan can be used to demonstrate some of the simpler aspects ofthe optimization of molecular geometry Computational Chemistry 81109 27 2a 2b At some point it will be expedient to discuss and illustrate in semi quantitative terms the other energy calculating strategies that employ the methods of quantum mechanics In this and several other situations we should not try to preempt the upper division courses In general the material that we cover in the computer laboratory will be at the level found in the more challenging general chemistry texts Any embellishment needs to be planned as a means of creating a seamless transition from the freshman curriculum to the sophomore orjunior experience Bond energies A strategy can be devised in which the MM energy of a diatomic molecule is investigated Different values are selected for the inter nuclear distance and single point energies calculated These energies can be plotted as a function of distance and the distance equilibrium bond length for the minimum energy determined One can also run a geometry optimization routine to verify that bond length Bond angles One may start with a non linear triatomic molecule like water for which the bond lengths and the bond angle have been optimized Keeping the bond lengths at their equilibrium values single point energies are then to be calculated for several values of the bond angle on either side of its equilibrium value Computational Chemistry 81109 2c 2c1 2c2 2c3 2d 28 Dihedral Angles There are several ways in which the energy associated with a dihedral angle might be explored szrazine We can create a hydrazine HNNH molecule with different values ofthe dihedral angle after the bond lengths have been optimized Single point energies may then be plotted as a function ofangle Ethane The distinct preference for staggered over eclipse structures can be shown in a number of ways By calculating and plotting single point energies for structures with optimized bond lengths but different dihedral angles we can see the roughly cosine formed potential energy curve 12 dichloroethane For this molecule or for nbutane we can explore the difference in energies for trans and guache conformers Steric effects We can use pentane or hexane as a simple example of a molecule for which steric effects van der Waals repulsions place limitations on the structural flexibility This involves starting with the all trans conformation and then gradually creating successive gauche orientations along the chain all in the same clock sense until inter atomic distances have become too short for stability Computational Chemistry 81109 29 2e 2f Internal hydrogen bonding Examples can be found of isomeric pairs of molecule where one derives extra stability from internal hydrogen bonding Internal dipole dipole stabilization We can also nd examples of molecules that derive enhanced stability in selective conformations from the existence of internal dipole dipole attractions IN TERMOLE CULAR ENERGY Investigating the nature and impact of intermolecular forces requires the use of docking or merging procedures These can be fairly easily learned and constitute an important skill in handling molecular modeling software 3a Dipole dipole forces of attraction One can look at the energies of interaction between pairs of dipolar molecules in both attractive and repulsive mutual orientations These can be compared with the energy of two completely separated moleculeS 3b London polarizibility forces The energies of interaction of pairs of homonuclear diatomic molecules might be estimated using a variety of different computational strategies Computational Chemistry 81109 30 3c Dipole induced Dipole attractions An attempt will be made to determine the energy of the interaction between a dipolar diatomic molecule like HCl and a non polar one like Br2 3d Hydrogen bonding It is instructive to examine the hydrogen bonding stabilization of water with a variety of polar groups in simple organic molecules 4 CRYSTAL STRUCTURES Computer generated images can be used to provide a good introduction to the nature of crystal symmetry and crystal structure 4a Unit Cells and crystal systems Examples will be found of each of the seven crystal systems The ability to change the orientation of the screen image is a great help in gaining an understanding of the different possible shapes of unit cells 4b Bravais lattices cubic close packing and formula units per unit cell There is software available for showing the nature of different types of lattices that correspond to a single crystal system Particular attention is paid to the three cubic lattices since they are the easiest to visualize Rationales can be given for the adoption of the different lattice schemes by alkali halides in terms of ionic size An explanation can be offered as to how one can combine density data with knowledge ofthe unit cell dimensions to determine the number of formula units per unit cell Computational Chemistry 81109 31 4c Diffraction and basic Xray crystallography Software may be located to demonstrate the principles involved in diffraction by a a double slit b a grating and c a crystal lattice There is no intention of getting involved in the ner details of crystal structure but a brief mention of the meaning and signi cance of key terms like Miller indices symmetry elements and space groups would be in order 5 FINGERPRIN TING Qualitative chemical analysis has been greatly facilitated by the use of instrumental techniques These are referred to as ngerprinting techniques 5a Infrared Spectroscopy Molecules and polyatomic ions are in a constant state of vibrational motion The molecules can become vibrationally excited by absorbing energy in the form of infrared radiation The molecules are selective in the wavelengths of radiation that they can absorb An infrared spectrometer provides us with a plot of the wavelengths of radiation that are absorbed and the relatively absorbances The plot of absorbance against wavelength or frequency constitutes a ngerprint of that molecular species The fingerprints can be used in a couple of ways One can take note of the speci c wavelengths where there is signi cant absorption There is an association between the functional groups of atoms in organic molecules and speci c regions of the infrared absorption spectrum This tells us the type of molecule that we are dealing with Computational Chemistry 81109 32 There are also data bases of infra red spectra The Sadtler directory of infra red spectra came in several printed volumes but it is now available on CDs 5b Nuclear Magnetic Resonance Spectra Atomic nuclei perform a spinning motion This motion generates a magnetic eld with values that are proportional to a spin quantum number For the humble proton there are two spin states with quantum numbers either 12 or 12 In the presence of a magnetic eld the two states have different energies Protons in the lower energy state can be excited to the higher by absorbing radio frequency radiation Protons in different local environments in the same molecule require different frequencies of radiation to be excited in this way for a speci c magnetic eld strength Alternatively different magnetic eld strengths will be required to create the same energy difference In either case we can record a proton magnetic resonance spectrum for a compound That spectrum is another fingerprint of the molecules involved It is also possible to obtain nuclear magnetic resonance spectra for 13C nuclei This provides an additional ngerprint 5c PowderX Ray patterns When a beam of Xrays encounters a sample ofa powdered solid it gives rise to a diffraction interference pattern A powder pattern consists of a set of rings of differing intensities For X radiation of a given wavelength one can obtain a plot of the intensities of the Computational Chemistry 81109 33 diffraction rings as a function of the angle of de ection from the original beam direction This plot serves as a third type of fingerprint Obviously it is particularly well suited to solid samples One can purchase a computer data base that makes it relatively simple to match the ngerprint of an unknown sample with its previously recorded counterpart 7 DA TA TREA TMEN T There are numerous factors that need to be taken into consideration when dealing with chemical or physical data 1 2 It is important to keep a record of all measurements as they are collected That includes not only the values of the measured properties but the conditions under which the measurements were made Before the advent of automatic data collection it was considered to be mandatory to enter by hand each observation into a hard bound notebook In many types of experiments that is still a reasonable requirement Where it would clearly be ridiculous and counter productive to hand copy vast amounts of computer accumulated data it should still be required that a hard copy should be made That hard copy should be identi ed as the raw data It should be signed and dated by the person gathering the data and the immediate supervisor if that is appropriate One should certainly keep a Journal It is a good practice to monitor the data as it is being accumulated lfone considers the kind of situation where one is making measurements under Computational Chemistry 81109 34 3 4 conditions where one controlled variable concentration temperature etc is being varied it is good practice to plot the data as each point is added Monitoring the data collection process permits one to assess whether or not the measurement procedure is going according to plan It can also give an indication of whether the measurements need to be taken at smaller or larger intervals in the controlled variable It is quite rare for chemists to accumulate data for the sole purpose of creating more tables of numbers to add to the literature More often than not the experiments are motivated by a desire to improve our understanding of the nature of reaction mixtures solutions or pure substances In order to judge the success ofthe operation one needs to do a number ofthings a One should try to make an assessment of whether or not the data that has been collected is of suf cient quality to furnish the chemical answers that one seeks b One should try to nd from the literature a valid theory for transforming the quantities that are actually measured into physical properties of the system that one is dealing with c A means needs to be found for providing a statistical estimate ofthe reliability ofthe ultimate answers We need to distinguish between two aspects of data handling We use the term data reduction when we subject each and every data point to the same algebraic manipulation We might quote as an example an investigation of the molar volumes of a pure solid substance at different temperatures The primary data might well be in the form of the measured densities Each density can then be transformed into the corresponding molar volume by the equation vm Mm p Where Mm is the molar mass and p is the density Computational Chemistry 81109 35 51 52 53 54 This is the kind of operation that is very conveniently performed using a spreadsheet No efforts are made at this stage to summarize the data and no assumptions are made as to the manner in which the molar volumes might vary with temperature Fitting analytic functions to sets of data provides one or more useful sources of information A plot ofthe tted curve and the data on the same axes will tell us whether or not the analytic function that we adopted is appropriate Provided that the choice of function was acceptable we can obtain statistical measures of the internal consistency ofthe data The parameters of the analytic function provide us with a convenient way of summarizing our observations For example if we find that we can do a decent job of fitting the data set yx with a function y a bx then we can describe the data by giving the equation the values of the parameters a and b and the standard deviation of the data points from the fitted straight line Quite frequently one may choose to use a function that is based upon a creditable theory to t the data In such cases the parameters will have some special physical significance Theories of propagation of errors allow us to translate the imperfections in the data to limits of con dence for these physical parameters We may look at several different software packages for handling and analyzing data Since we will not be able to spend more than a few hours in this initial learning stage we will not be able to explore all of the capabilities of even one
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