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  • Loren Williams Research
    2 10 MB data link hi res at Iron Man RNA World jpg data isimage true data width 525 data height 720 17 Iron Man and the RNA World unam poster 2013 data size 586 32 kB data link hi res unam poster 2013 jpg data isimage true data width 509 data height 720 18 DNA chemical structure data size 429 98 kB data link hi res DNA chemical structure jpg data isimage true data width 447 data height 720 19 cg basepair data size 113 03 kB data link hi res cg basepair jpg data isimage true data width 960 data height 658 20 at basepair data size 101 78 kB data link hi res at basepair jpg data isimage true data width 960 data height 461 21 DNA double helix data size 564 90 kB data link hi res DNA double helix jpg data isimage true data width 496 data height 720 22 watson crick dna data size 71 24 kB data link hi res watson crick dna jpg data isimage true data width 278 data height 720 23 duplex high res map data size 3 23 MB data link hi res duplex high res map jpg data isimage true data width 446 data height 720 24 vda phosphate clamp data size 61 01 kB data link hi res vda phosphate clamp jpg data isimage true data width 600 data height 421 25 gla six coord data size 108 10 kB data link hi res gla six coord jpg data isimage true data width 600 data height 368 26 vdb triplatin nc data size 202 46 kB data link hi res vdb triplatin nc jpg data isimage true data width 400 data height 720 27 h5 stack data size 157 34 kB data link hi res h5 stack jpg data isimage true data width 211 data height 720 28 h4 wp631 data size 153 28 kB data link hi res h4 wp631 jpg data isimage true data width 304 data height 720 29 h4 nog data size 124 29 kB data link hi res h4 nog jpg data isimage true data width 600 data height 706 30 h3 tota data size 165 45 kB data link hi res h3 tota jpg data isimage true data width 530 data height 720 31 h1 adria tl data size 134 05 kB data link hi res h1 adria tl jpg data isimage true data width 597 data height 720 32 go cosb 2 data size 74 59 kB data link hi res go cosb 2 jpg data isimage true data width 600 data height 334 33 go cgcgaattcgcg tl data size 177 97 kB data link hi res go cgcgaattcgcg tl jpg data isimage true data width 442 data height 720 34 glb p22 minor groove coordination The minor groove data size 512 73 kB data link hi res glb p22 minor groove coordination jpg data isimage true data width 960 data height 472 35 The minor groove ft A tract

    Original URL path: http://ww2.chemistry.gatech.edu/~williams/bResearch_Interests/index.htm (2015-06-03)
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  • Williams Group
    430 69 Deep discussion 2011 Nick Hud and friends Emily went to vet school at UGa Emily McManus data size 1 12 MB data link DSCN1666 JPG data isoriginal true data isimage true data width 720 data height 540 70 Emily went to vet school at UGa Emily McManus Loren his post doc advisor Alex Rich and Loren Williams data size 553 89 kB data link Alex Rich Loren Williams Albany JPG data isoriginal true data isimage true data width 720 data height 588 71 Loren his post doc advisor Alex Rich and Loren Williams Jessie went to grad school at UCSD Jessie Peters undergraduate data size 205 17 kB data link jessie peters 2011 jpg data isoriginal true data isimage true data width 720 data height 720 72 Jessie went to grad school at UCSD Jessie Peters undergraduate 19th Annual Suddath Symposium 2011 Caitlin Prickett Steve Harvey Ada Yonath and Lively Lie data size 1 79 MB data link 19th Annual Suddath Symposium 04012011 73 JPG data isoriginal true data isimage true data width 720 data height 474 73 19th Annual Suddath Symposium 2011 Caitlin Prickett Steve Harvey Ada Yonath and Lively Lie 19th Annual Suddath Symposium 2011 Tatsuya Maehigashi graduate student Taylor Updegrove graduate student w RW Jessie Peters undergraduate Jason Murray undergraduate Lively Lie graduate student w RW Caitlin Prickett technician data size 1 40 MB data link 19th Annual Suddath Symposium 04012011 88 JPG data isoriginal true data isimage true data width 720 data height 505 74 19th Annual Suddath Symposium 2011 Tatsuya Maehigashi graduate student Taylor Updegrove graduate student w RW Jessie Peters undergraduate Jason Murray undergraduate Lively Lie graduate student w RW Caitlin Prickett technician Kayaking 2011 Derrick Watkins graduate student data size 1 22 MB data link derrick watkins JPG data isoriginal true data isimage true data width 720 data height 439 75 Kayaking 2011 Derrick Watkins graduate student RiboEvo Summer Camp Life in the Extreme 2011 Students and instructors data size 2 24 MB data link 2011 nasa camp all jpg data isoriginal true data isimage true data width 720 data height 591 76 RiboEvo Summer Camp Life in the Extreme 2011 Students and instructors at UVa Cameron Mura Undergraduate Linda Columbus data size 96 17 kB data link cameron mura linda columbus jpg data isoriginal true data isimage true data width 520 data height 512 77 at UVa Cameron Mura Undergraduate Linda Columbus Carl Pilcher former NAI director 2011 Carl Pilcher Loren Williams data size 611 35 kB data link carl pilcher loren williams JPG data isoriginal true data isimage true data width 627 data height 720 78 Carl Pilcher former NAI director 2011 Carl Pilcher Loren Williams 2011 Catherine Tripp Undergraduate Jason Murray Undergraduate data size 362 19 kB data link Catherine Tripp and Jason Murray JPG data isoriginal true data isimage true data width 720 data height 483 79 2011 Catherine Tripp Undergraduate Jason Murray Undergraduate 2011 Gary Longstreet Jim Powers data size 1 06 MB data link DSC00076 JPG data isoriginal true data isimage true data width 720 data height 406 80 2011 Gary Longstreet Jim Powers Went to med school Caitlin Prickett technician data size 486 67 kB data link Caitlin Prickett jpg data isoriginal true data isimage true data width 642 data height 720 81 Went to med school Caitlin Prickett technician Went to med school Caitlin Prickett technician data size 597 97 kB data link Caitlin Prickett 2 jpg data isoriginal true data isimage true data width 635 data height 720 82 Went to med school Caitlin Prickett technician PhD with Steve Harvey Yingying Zhen data size 516 28 kB data link Yingying Zeng JPG data isoriginal true data isimage true data width 610 data height 720 83 PhD with Steve Harvey Yingying Zhen Went to work for Dev Arya s company Derrick Watkins graduate student data size 555 18 kB data link derrick watkins 1 jpg data isoriginal true data isimage true data width 581 data height 720 84 Went to work for Dev Arya s company Derrick Watkins graduate student Manny left us in 2012 Emmanuel Tannenbaum June 28 1978 May 28 2012 data size 47 16 kB data link manny 1 jpg data isoriginal true data isimage true data width 401 data height 492 85 Manny left us in 2012 Emmanuel Tannenbaum June 28 1978 May 28 2012 Got tenure 2013 Raquel Lieberman data size 282 70 kB data link Raquel Liberman JPG data isoriginal true data isimage true data width 540 data height 720 86 Got tenure 2013 Raquel Lieberman Steve Harvey s Birthday Party 2010 Steve did not show up for his birthday party so we ate the cake without him data size 644 95 kB data link Steve Harvey Bday JPG data isoriginal true data isimage true data width 720 data height 449 87 Steve Harvey s Birthday Party 2010 Steve did not show up for his birthday party so we ate the cake without him Diya went to postdoc for Harry Noller Graduation Srividya Mohan graduate student data size 38 04 kB data link srividya mohan graduation jpg data isoriginal true data isimage true data width 276 data height 376 88 Diya went to postdoc for Harry Noller Graduation Srividya Mohan graduate student Opening the CCE Nick Hud data size 508 01 kB data link nick hud jpeg data isoriginal true data isimage true data width 720 data height 697 89 Opening the CCE Nick Hud Williams Group 2007 Diya Mohan graduate student Chiaolong Hsiao graduate student Tatsuya Maehigashi graduate student Derrick Watkins graduate student data size 325 02 kB data link Williams Group 2007 2 JPG data isoriginal true data isimage true data width 720 data height 648 90 Williams Group 2007 Diya Mohan graduate student Chiaolong Hsiao graduate student Tatsuya Maehigashi graduate student Derrick Watkins graduate student Williams Group 2007 Chiaolong Hsiao graduate student Diya Mohan graduate student Tatsuya Maehigashi graduate student Loren Williams Derrick Watkins graduate student data size 272 33 kB data link Williams Group 2007 JPG data isoriginal true data isimage true data width 720 data height 526 91 Williams Group 2007 Chiaolong Hsiao graduate student Diya Mohan graduate student Tatsuya Maehigashi graduate student Loren Williams Derrick Watkins graduate student Audra went to med school Audra Morabito Robinson undergraduate Derrick Watkins graduate student data size 139 43 kB data link Audra Morabito Derrick Watkins jpg data isoriginal true data isimage true data width 641 data height 363 92 Audra went to med school Audra Morabito Robinson undergraduate Derrick Watkins graduate student works at US Army Medical Research Institute of Infectious Diseases Tinoush Moulaei graduate student data size 278 33 kB data link tinoush 1 jpg data isoriginal true data isimage true data width 565 data height 576 93 works at US Army Medical Research Institute of Infectious Diseases Tinoush Moulaei graduate student T went to post doc at Emory Tatsuya Maehigash graduate student data size 160 93 kB data link t jpg data isoriginal true data isimage true data width 678 data height 720 94 T went to post doc at Emory Tatsuya Maehigash graduate student Buzz 2004 Diya Mohan graduate student Buzz data size 155 92 kB data link sri mohan jpg data isoriginal true data isimage true data width 376 data height 556 95 Buzz 2004 Diya Mohan graduate student Buzz Ramblin Wreck 2004 Trudy the Rambling Wreck data size 116 11 kB data link trudy walker jpg data isoriginal true data isimage true data width 707 data height 468 96 Ramblin Wreck 2004 Trudy the Rambling Wreck Nick s post doc Irena Mamajanova data size 280 52 kB data link DSC 0109 jpg data isoriginal true data isimage true data width 375 data height 720 97 Nick s post doc Irena Mamajanova does our accounts Mamie Gaskin data size 992 32 kB data link Mamie Gaskin jpg data isoriginal true data isimage true data width 607 data height 720 98 does our accounts Mamie Gaskin Tatsuya Maehigashi Tatsuya Maehigashi graduate student data size 97 80 kB data link T 2 jpg data isoriginal true data isimage true data width 622 data height 720 99 Tatsuya Maehigashi Tatsuya Maehigashi graduate student 2007 Barbara was Loren s PhD advisor MIckey was Barbara s PhD advisor Loren Williams Barbara Ramsay Shaw and Mickey Schurr data size 90 33 kB data link schurr brs ldw 2007 jpg data isoriginal true data isimage true data width 529 data height 392 100 2007 Barbara was Loren s PhD advisor MIckey was Barbara s PhD advisor Loren Williams Barbara Ramsay Shaw and Mickey Schurr at UCLA 2010 Diya Mohan graduate student data size 408 49 kB data link Srividya Mohan UCLA JPG data isoriginal true data isimage true data width 630 data height 720 101 at UCLA 2010 Diya Mohan graduate student Tinoush Moulaei Tinoush Moulaei graduate student data size 184 73 kB data link tinoush a1 jpg data isoriginal true data isimage true data width 441 data height 720 102 Tinoush Moulaei Tinoush Moulaei graduate student went to be a Professor at Suzuka University of Medical Science Seiji Komeda postdoc data size 100 25 kB data link seiji 1 jpg data isoriginal true data isimage true data width 620 data height 720 103 went to be a Professor at Suzuka University of Medical Science Seiji Komeda postdoc Williams Group 2001 Denise Jone s PhD celebration Brian Lynch graduate student Shelley Howerton graduate student Sarah Tannanbaum Melissa Kerzic graduate student Kris Woods graduate student Loren Williams Denise Jones Gregory graduate student Shawn Gregory data size 1 29 MB data link group 2001a jpg data isoriginal true data isimage true data width 720 data height 400 104 Williams Group 2001 Denise Jone s PhD celebration Brian Lynch graduate student Shelley Howerton graduate student Sarah Tannanbaum Melissa Kerzic graduate student Kris Woods graduate student Loren Williams Denise Jones Gregory graduate student Shawn Gregory Williams Group 2002 Loren Williams Kris Woods graduate student Billy Booth graduate student Mary Peek graduate student Sarah Tannenbaum undergraduate Tinoush Moulaei graduate student Eli Hershkovits research scientist Derrick Watkins graduate student data size 359 23 kB data link research group 2002 JPG data isoriginal true data isimage true data width 720 data height 719 105 Williams Group 2002 Loren Williams Kris Woods graduate student Billy Booth graduate student Mary Peek graduate student Sarah Tannenbaum undergraduate Tinoush Moulaei graduate student Eli Hershkovits research scientist Derrick Watkins graduate student Williams Group 2001 Akanksha Nagpol graduate student Shelley Howerton graduate student Kevin Maloney summer undergraduate Kris Woods graduate student Dan Schnobrich summer undergraduate Tinoush Moulaei graduate student Melissa Kerzic graduate student Ryan Burnette graduate student Loren Williams data size 306 73 kB data link group 2001 jpg data isoriginal true data isimage true data width 720 data height 442 106 Williams Group 2001 Akanksha Nagpol graduate student Shelley Howerton graduate student Kevin Maloney summer undergraduate Kris Woods graduate student Dan Schnobrich summer undergraduate Tinoush Moulaei graduate student Melissa Kerzic graduate student Ryan Burnette graduate student Loren Williams Williams Group 2001 Perry and Ryan Burnette graduate student Melissa Kerzic graduate student Dan Schnobrich summer undergraduate Loren Justin Nidhi data size 293 38 kB data link group a 2001 jpg data isoriginal true data isimage true data width 720 data height 497 107 Williams Group 2001 Perry and Ryan Burnette graduate student Melissa Kerzic graduate student Dan Schnobrich summer undergraduate Loren Justin Nidhi DSC01064 Tinoush Moulae graduate student data size 251 60 kB data link DSC01064 JPG data isoriginal true data isimage true data width 369 data height 637 108 Tinoush Moulae graduate student Tinoush Moulaei Tinoush Moulaei graduate student data size 252 50 kB data link tinoush 2 jpg data isoriginal true data isimage true data width 523 data height 720 109 Tinoush Moulaei Tinoush Moulaei graduate student Tinoush Moulaei Tinoush Moulaei graduate student data size 298 34 kB data link DSC01080 JPG data isoriginal true data isimage true data width 468 data height 695 110 Tinoush Moulaei Tinoush Moulaei graduate student Williams group 2001 RH side Nidhi Williams Melissa Kerzic graduate student Perry Ryan Burnett graduate student LH side Kevin Maloney Dan Schnobrich both summer undergraduates data size 250 71 kB data link research group bus 2001 jpg data isoriginal true data isimage true data width 720 data height 445 111 Williams group 2001 RH side Nidhi Williams Melissa Kerzic graduate student Perry Ryan Burnett graduate student LH side Kevin Maloney Dan Schnobrich both summer undergraduates 2001 Kevin Maloney summer undergraduate data size 263 35 kB data link kevin maloney a 2001 jpg data isoriginal true data isimage true data width 388 data height 720 112 2001 Kevin Maloney summer undergraduate 2001 Perry Ryan Burnett graduate student data size 137 64 kB data link ryan burnett 2001 jpg data isoriginal true data isimage true data width 720 data height 335 113 2001 Perry Ryan Burnett graduate student 2001 Melissa Kerzic graduate student data size 127 76 kB data link melissa kerzic a 2001 jpg data isoriginal true data isimage true data width 642 data height 583 114 2001 Melissa Kerzic graduate student brian Brian Lynch graduate student data size 275 98 kB data link brian jpg data isoriginal true data isimage true data width 504 data height 555 115 Brian Lynch graduate student 2000 Kris teaches at Bradley University Kris Woods graduate student data size 254 24 kB data link kris 1 jpg data isoriginal true data isimage true data width 499 data height 576 116 2000 Kris teaches at Bradley University Kris Woods graduate student 2000 Kris teaches at Bradley University Kris Wood graduate student data size 222 60 kB data link kris 2 jpg data isoriginal true data isimage true data width 458 data height 576 117 2000 Kris teaches at Bradley University Kris Wood graduate student 2000 Shelley Howerton graduate student data size 369 48 kB data link DSC01086 JPG data isoriginal true data isimage true data width 576 data height 621 118 2000 Shelley Howerton graduate student 2002 Shelley Howerton graduate student data size 240 55 kB data link shelley 2 jpg data isoriginal true data isimage true data width 504 data height 500 119 2002 Shelley Howerton graduate student Denise teaches at Samford University Denise Jones Gregory graduate student data size 181 26 kB data link denise jones 1 jpg data isoriginal true data isimage true data width 432 data height 513 120 Denise teaches at Samford University Denise Jones Gregory graduate student Shelley teaches in the Cobb School District Shelley Howerton graduate student data size 192 50 kB data link shelley 3 jpg data isoriginal true data isimage true data width 576 data height 440 121 Shelley teaches in the Cobb School District Shelley Howerton graduate student Chad works at Omniscribe Chad SInes graduate student data size 324 03 kB data link chad 2 jpg data isoriginal true data isimage true data width 576 data height 658 122 Chad works at Omniscribe Chad SInes graduate student Went to Mercer Med School Audra Morabito Undergraduate data size 343 77 kB data link Audra Morabito jpg data isoriginal true data isimage true data width 720 data height 651 123 Went to Mercer Med School Audra Morabito Undergraduate Roles of Metals in Biological Reactions Biology and Medicine Kyoto 2005 Nick Farrell collaborator data size 270 24 kB data link nick farrell jpg data isoriginal true data isimage true data width 400 data height 720 124 Roles of Metals in Biological Reactions Biology and Medicine Kyoto 2005 Nick Farrell collaborator 2002 Brian Lynch graduate student data size 253 66 kB data link brian 2 jpg data isoriginal true data isimage true data width 435 data height 648 125 2002 Brian Lynch graduate student 2002 Chad Sines graduate student data size 210 29 kB data link chad jpg data isoriginal true data isimage true data width 504 data height 387 126 2002 Chad Sines graduate student Dr Protease Jim Powers collaborator colleague data size 193 82 kB data link DSC00739 JPG data isoriginal true data isimage true data width 360 data height 622 127 Dr Protease Jim Powers collaborator colleague Williams Group 2000 Loren Williams with Justin Melissa Kerzic graduate student Kris Woods graduate student Brian Lynch graduate student Denise Jones Gregory graduate student Shelley Howerton graduate student Laura Howeton Front Tinoush Moulaei graduate student data size 441 84 kB data link group 5 00 JPG data isoriginal true data isimage true data width 720 data height 545 128 Williams Group 2000 Loren Williams with Justin Melissa Kerzic graduate student Kris Woods graduate student Brian Lynch graduate student Denise Jones Gregory graduate student Shelley Howerton graduate student Laura Howeton Front Tinoush Moulaei graduate student Brian Lynch Brian Lynch graduate student data size 234 77 kB data link DSC01089 JPG data isoriginal true data isimage true data width 576 data height 517 129 Brian Lynch Brian Lynch graduate student DSC01061 data size 322 57 kB data link DSC01061 JPG data isoriginal true data isimage true data width 287 data height 720 130 2000 Shelly Howerton front graduate student data size 382 22 kB data link DSC01047 JPG data isoriginal true data isimage true data width 720 data height 459 131 2000 Shelly Howerton front graduate student Williams and Wartell groups 2000 data size 326 29 kB data link lw rw fd JPG data isoriginal true data isimage true data width 720 data height 324 132 Williams and Wartell groups 2000 Williams and Wartell groups 2000 data size 353 43 kB data link DSC01049 JPG data isoriginal true data isimage true data width 720 data height 488 133 Williams and Wartell groups 2000 Williams and Wartell groups 2000 data size 236 36 kB data link DSC01054 JPG data isoriginal true data isimage true data width 720 data height 312 134 Williams and Wartell groups 2000 Marc Vogt Marc Vogt data size 191 67 kB data link mark vogt jpg data isoriginal true data isimage true data width 432 data height 506 135 Marc Vogt Marc Vogt went to UGA law school Russell Blythe undergraduate data size 228 22 kB

    Original URL path: http://ww2.chemistry.gatech.edu/~williams/bResearch_Group/index.html (2015-06-03)
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  • Molecular Interactions (Noncovalent Interactions)
    on the polarizability of the second molecule Dipole induced dipole interactions are important even between two molecules that both have permanent dipoles A permanent dipole is changed by the dipole of an adjacent molecule For example in liquid water where molecules are close together all water molecules are polarized The permanent dipole of each water molecule polarizes all adjacent water molecules The dipole of a water molecule induces a change in the dipole of a nearby water molecule compared to the permanent dipole of an isolated water molecule in the gas phase Figure 11 shows how water molecules polarize each other Each water molecule polarizes neighboring water molecules and increases neighboring dipole moments When the two water molecules approach each other and form a hydrogen bond as shown here the partial negative charge on the oxygen of the top water molecule is increased in magnitude and the partial positive charge on the proton of the bottom water molecule is also increased Here the symbol size is scaled to the magnitude of the partial charge Dipole induced dipole interactions are always attractive and can contribute as much as 0 5 kcal mole to stabilization of molecular associations Dipole induced dipole interactions fall off with 1 r 4 Formally charged species Na Mg 2 COO etc also polarize nearby molecules and induce favorable dipoles The resulting interactions called charge induced dipole interactions or ion induced dipole interactions These interactions are important for example in protein structure but are not broken out into a separate section in this document D4 Dipole charge interactions Table of Contents Structure Tool Williams Home A molecule with a permanent dipole can interact favorably with cations and anions This type of interaction is called a dipole charge or ion dipole interaction Dipole charge interactions are why sodium chloride composed cationic sodium ions and anionic chloride ions and other salts tend to interact well with water and are very soluble in water which has a strong dipole Figure 12 shows four water molecules interacting favorably with a magnesium dication The negative ends of the water dipoles are directed toward the positively charged magnesium ion If the ion is an anion such as chloride the water molecules switch direction and direct the positive ends of their dipoles toward the anion Here the dashed lines do not represent hydrogen bonds There are no hydrogen atoms between the Mg 2 cation and the water oxygen atoms E Fluctuating dipoles Dispersive interactions London Forces Table of Contents Structure Tool Williams Home We can see resonance all around us A child on a swing the tides in the Bay of Fundy and the strings on a violin all illustrate natural resonant frequencies of physical systems The Tacoma Narrows Bridge is one of the most famous examples of resonance Molecules resonate too Electrons even in a spherical atom like Helium or Xenon fluctuate over time according to the natural resonant frequency of that atom Even though chemists describe atoms like Helium and Xenon as spherical if you could take a truly instantaneous snapshot of one of these atoms you would always catch it in a transient non spherical state Xenon is spherical on average but not at any instantaneous timepoint Fluctuating electrons cause fluctuating dipoles When the instantaneous electron density of a molecule or atom fluctuates the dipole moment also fluctuates Therefore molecules and atoms behave like oscillating dipoles In molecules that are located nearby to each other the oscillating dipoles sense each other and couple They oscillate in synch The movements of the electrons in adjacent molecules are correlated Electrons in one atom tend to run away from those in the next because of electrostatic repulsion Coupled fluctuating dipoles experience favorable electrostatic interaction known as dispersive interactions The strength of the interaction is related to the polarizabilities of the two molecules or atoms Figure 13 shows how fluctuating dipoles of liquid Xenon or Helium or Neon etc are coupled Darker blue indicates higher electron density The fluctuations are correlated and are very fast on the femtosecond 10 15 second timescale Adjacent Xenon atoms experience electrostatic attraction from the transient dipoles Two different representations of fluctuating dipoles are shown Dispersive interactions are always attractive and occur between any pair of molecules polar or non polar that are nearby to each other Dispersive interactions are the only attractive forces between atoms in liquid He bp 4 5 K Ne 27K Ar 87K and between molecules of N 2 77K Without dispersive interactions there would be no liquid state for the Nobles About a 25 of the attractive forces between water molecules are dispersive in nature The total number of pairwise atom atom dispersive interactions within a folded protein is enormous so that dispersive interactions can make a large contribute to stability Fluctuating dipole interactions fall off with 1 r 6 F Hydrogen Bonding F1 General Description of Hydrogen Bonds Table of Contents Structure Tool Williams Home The idea that a single hydrogen atom could bond simultaneously to two other atoms was proposed in 1920 by Latimer and Rodebush and their advisor G N Lewis Maurice Huggins who was also a student in Lewis lab describes the hydrogen bond in his 1919 dissertation Figure 14 illustrates the elements of a hydrogen bond including the HB acceptor and HB donor the lone pair and the acidic proton N O S are the predominant hydrogen bonding atoms A D in biological systems An atom A containing a basic lone pair of electrons i e a Lewis Base can interact favorably with a hydrogen atom H that is covalently bound to a donor atom D A hydrogen bond requires that atoms A and D are both electronegative H D must have acidic properties In a hydrogen bond the Lewis Base A is called hydrogen bond acceptor and the acidic group H D is called the hydrogen bond donor Hydrogen is the only atom that i forms covalent bonds with electronegative atoms like N and O and ii uses the inner shell 1S electron s for bonding When its bonding partner pulls electrons away from hydrogen the nucleus a proton is exposed on the back side distal from the bonding partner An unshielded proton is thus available for electrostatic interactions with electron lone pairs Hydrogen is the only atom that exposes its nucleus this way Other atoms have inner shell non bonding electrons that shield the nucleus The salient features of a generic hydrogen bond are illustrated in the figure above A hydrogen bond is not an acid base reaction where the proton H is fully transferred from H D to A to form D and HA However the strength of a hydrogen bond correlates well with the acidity of donor H D and the basicity of acceptor A In a hydrogen bond the H is partially transfered from H D to A but H remains covalently attached to D The H D bond remains intact Figure 15a illustrates three different styles for representing a hydrogen bond Atom A is the Lewis base for example the N in NH 3 or the O in H 2 O and the atom D is electronegative for example O N or S The conventional nomenclature is confusing a hydrogen bond is not a covalent bond The most common hydrogen bonds in biological systems involve oxygen and nitrogen atoms as A and D Keto groups O amines R 3 N imines R N R and hydroxyl groups OH are the most common hydrogen bond acceptors in DNA RNA proteins and complex carbohydrates Hydroxyl groups and amines imines are the most common hydrogen bond donors Hydroxyls and amines imines can both donate and accept hydrogen bonds Figure 15b shows the most common hydrogen bond acceptors and donors in biological macromolecules In traversing the Period Table increasing the electronegativity of atom D strips electron density from the proton in H D increasing its partial positive charge and increasing the strength of any hydrogen bond Thiols SH can can both donate and accept hydrogen bonds but these are generally weak because sulfur is not sufficiently electronegative Hydrogen bonds involving carbon where H D equals H C are observed although these are weak and infrequent C is insufficiently electronegative to form good hydrogen bonds Hydrogen bonds are essentially electrostatic in nature although the energy can be decomposed into additional contributions from polarization exchange repulsion charge transfer and mixing Hydrogen bond strengths form a continuum Strong hydrogen bonds of 20 40 kcal moll generally formed between charged donors and acceptors are nearly as strong as covalent bonds Weak hydrogen bonds of 1 5 kcal mol sometimes formed with carbon as the proton donor are no stronger than conventional dipole dipole interactions Moderate hydrogen bonds which are the most common are formed between neutral donors and acceptors are from 3 12 kcal mol F2 Geometry of Hydrogen Bonds Table of Contents Structure Tool Williams Home The geometry of a hydrogen bond can be described by three quantities the D to H distance the H to A distance and the D to H to A angle The distances depend on the atom types of A and D If both A and D are oxygen atoms then optimally H to A 1 8 Å and D to H 1 0 Å The most stable hydrogen bonds are close to linear D to H to A angle of 180 The hydrogen bonds in antiparallel β sheets are linear while the hydrogen bonds in parallel β sheets are non linear Figure 16 illustrates the non linearity of parallel β sheet hydrogen bonds and the linearity of antiparallel β sheet hydrogen bonds Hydrogen bonds can be two center as in a β sheets and ideal ice three center or four center Two center hydrogen bonds are generally shorter more linear and stronger than three or four center hydrogen bonds Three center bonds are sometimes called bifurcated while four centered hydrogen bonds are sometimes called trifurcated Figure 17 illustrates two three and four center hydrogen bonds The two center hydrogen bond is closest to an ideal hydrogen bond and is stronger than the other types The left hand four center hydrogen bonding scheme is observed in crystalline ammonium where one acceptor lone pair has to accomodate three donors see section on ammonia below Hydrogen atoms are not observable by x ray crystallography as applied to proteins and nucleic acids So a geometric description of hydrogen bonding that is dependent on the proton position is not practical in protein and nucleic acid structures In these cases one is usually limited to analysis of the D to A distance It is common to ascribe a hydrogen bond if a distance between A and D is less than the sum of their van der Waal radii However this limit is probably too conservative The best criteria for an H bond is a distance of less than 3 4 Å between D and A F3 Hydrogen Bonding in Water Table of Contents Structure Tool Williams Home An isolated molecule of water H 2 O can form strong hydrogen bonds with either hydrogen bond donors or acceptors One water molecule can accept two hydrogen bonds and donate two hydrogen bonds or more if the hydrogen bonds are bifurcated or trifurcated Figure 18 Illustrates hydrogen bonding between two water molecules as observed in crystalline water ice The hydrogen bonds are short linear and strong These are two center hydrogen bonds Although each water molecule in ice forms four hydrogen bonds only one hydrogen bond is shown here Hydrogen bonds cause violations of van der Walls surfaces The hydrogen bonding distance from H to O is around 1 8 Å which is less than the sum of the O and H van der Waals radii r O 1 5 Å r H 1 0 Å Also notice that the hydrogen bonding distance from O to O is around 2 8 Å which is less than twice the van der Waals radius of oxygen r O 1 5 Å Figure 19 shows how hydrogen bonds link two water molecules This figure illustrates the difference between a covalent bond linking an oxygen atom to a hydrogen atom and a hydrogen bond also linking an oxygen to a hydrogen A hydrogen bond is a non covalent molecular interaction Oxygen atoms are red and hydrogen atoms are white The space filling representation on the right shows how hydrogen bonding causes violations of van der Waals surfaces Oxygen is highly electronegative and gains partial negative charge by withdrawing electron density from the two hydrogen atoms to which it is covalently bonded leaving them with partial positive charges Water has a balanced number of hydrogen bond donors and acceptors In ice every water molecule acts as a donor in two hydrogen bonds and an acceptor in two hydrogen bonds Water is an excellent hydrogen bonding solvent The coordinates of a water molecule linked by hydrogen bonds to two other water molecules are here coordinates Figure 20 illustrates that a water molecule can donate two hydrogen bonds and accept two hydrogen bonds The central water molecule here is donating two and accepting two hydrogen bonds In bulk liquid water the total number of hydrogen bond donors equals the total number of hydrogen bond acceptors All hydrogen bonding donors and acceptors are satisfied Water is self complementary The coordinates of a very small ice cube are here coordinates For additional information on water see the section on water and the hydrophobic effect F4 Hydrogen Bonding in Ammonia Table of Contents Structure Tool Williams Home A comparison of ammonia to water shows part of the significance of the self complementarity of water A single ammonia molecule NH 3 like a single water molecule can form strong hydrogen bonds with either hydrogen bond donors or acceptors However unlike water ammonia does not have a balanced number of hydrogen bond donors and acceptors Water is self complementary while ammonia is not A water molecule has equivalent numbers of acceptor and donor sites An ammonia molecule has more hydrogen bond donor sites than acceptor sites Yet in the crystalline state each ammonia molecule donates three and accepts three hydrogen bonds How does this happen To achieve six hydrogen bonds per ammonia molecule the single lone pair orbital on each nitrogen is shared by three hydrogen bond donors N H s of three adjacent ammonia molecules This hydrogen bond is trifucated as described above see figure All of these hydrogen bonds are sub optimal Each hydrogen bond in crystalline ammonia is long bent and weak 3 Hbond width 30 height 30 border 2 Figure 21 Illustrates the hydrogen bonding as observed in crystalline ammonia The hydrogen bonds are longer than those in ice and are non linear Although each ammonia molecule forms hydrogen bonds with six neighbors in the crystal only two ammonia molecules are shown here The boiling point of ammonia is 33 C much lower than that of water 100 C indicating that molecular interactions in NH 3 liq are significantly weaker than in H 2 O liq Although the number of hydrogen bonds per molecule is greater in solid liquid ammonia than in water the hydrogen bonds in water are much stronger The coordinates of an ammonia molecule are here coordinates F5 Cooperativity of Hydrogen Bonds Table of Contents Structure Tool Williams Home In biological systems hydrogen bonds are frequently cooperative In systems with multiple hydrogen bonds the strength of one hydrogen bond is increased by a adjacent hydrogen bond For example in the hydrogen bonded systems below the acetic acid dimer the top hydrogen bond increases both the acidity of the hydrogen and the basicity of the oxygen in the bottom hydrogen bond Each hydrogen bond makes the other stronger than it would be in isolation Cooperativity of hydrogen bonding is observed in base pairing and in folded proteins Figure 22 shows cooperativity via resonance of the hydrogen bonds of an acetic acid dimer top and of a G C base pair bottom Formation of one hydrogen bond increases the stability of an adjacent hydrogen bond and vice versa Figure 23 shows cooperativity via resonance of the hydrogen bonds of an anti parallel β sheet F6 Hydrogen Bonding in Molecular Recognition and Assembly Table of Contents Structure Tool Williams Home Because of their directionality tunability and ubiquity in simple organic molecules and biological polymers hydrogen bonding interactions are one of nature s most powerful devices of molecular recognition Hydrogen bonding donors and acceptors in complementary 2D and 3D arrays are observed in many biological assemblies The locations and directions of the donors and the acceptors are matched sometimes over vast surfaces However not all complementary surfaces in biology involve hydrogen bonds Leucine zippers between α helices are examples of complementary interactions that involve molecular interactions other than hydrogen bonds Figure 24 Self assembly of biological macromolecules is driven by complementary hydrogen bonding interactions Left Base pairing between complementary hydrogen bond donors and acceptors on the sidechains of nucleic acids Center Backbone assembly between self complementary hydrogen bond donors and acceptors of the protein backbone to form anti parallel β strands in a β sheet and Right Self complementary hydrogen bond donors and acceptors in carbohydrate between glucose moieties within cellulose F7 Hydrogen Bonding in Template Directed Catalysis Table of Contents Structure Tool Williams Home Biological systems have unique abilities to link complex molecular interactions to catalytic functions Sophisticated non covalent interactions control formation of covalent bonds Some of the most advanced forms of these phenomena are observed in DNA and RNA polymerases and in the ribosome In these systems hydrogen bonding and other molecular interactions direct catalytic function In an RNA polymerase if correct hydrogen bonding i e C G or A U T Watson Crick hydrogen bonding occurs between the template strand and the incoming nucleotide then the enzyme catalyzes formation of a covalent bond When wrong interactions e g a G U pair are detected the enzyme kicks out the incoming

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  • Macromolecular Structure
    Pymol Script Antiparallel β Sheet Pymol Script Loops and turns 5 Protein Folds Protein Folds Pymol Script Fibrous proteins Collagen Pymol Script α Helical proteins Albumin Pymol Script Myoglobin Pymol Script Hemoglobin Pymol Script Seven Transmembrane α Helices Pymol Script α Helical β Sheet proteins Carboxypeptidase Pymol Script Anti parallel β sheet proteins Porin Pymol Script parallel β sheet proteins HMW1 Adhesin Pymol Script 6 Protein Metal Interactions Metals radii coordinate numbers etc Calmodulin Pymol Script Potassium Channel 7 Protein Nucleotide Interactions Rossman Fold 8 Bases Nucleosides and Nucleotides ribose deoxyribose Syn Anti Pymol Script Sugar Pucker Pymol Script bases base pairs triplets and quartets 9a DNA Structure B DNA Pymol Script phosphodiester backbone DNA Torsion Angle Pymol Script Triplex Pymol Script A B Z conformation Supercoiling 9b RNA Structure ATP Pymol Script GNRA Tetraloops GNRA Tetraloop Pymol Script coordinates for 20 GNRA tetraloops Kink Turns Kink Turn Pymol Script tRNA tRNA Pymol Script Ribosome Small Subunit Pymol Script Thermus Thermophilus Ribosome Pymol Script motifs 10 Interactions of nucleic acids with small molecules Water Spine of Hydration Pymol Script Magnesium Spermine Minor groove binders Intercalators and Bis intercalators 11a Carbohydrate Images and Coordinates 11 Interactions of nucleic acids with proteins

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  • Crystallography Home Page
    Size and Wavelength 1 2 Symmetry Point Groups Lattices Lattices Bravais Lattices Space Groups Visualization Bragg Equation Waves Fourier Analysis Data Reduction Data Quality MIR Phases MIR Exercise Anomalous Scattering

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  • Williams Course List
    Protein and Nucleic Acid Structure CHEMISTRY 4511 Biochemistry I CHEMISTRY 6581 DNA Technology Nucleic Acid Biochemistry CHEMISTRY 1310 Introductory Chemistry CHEMISTRY 3511 Biochemistry CHEMISTRY 4581 Biochemistry Laboratory I Macromolecular Crystallography Chemistry 6582 Biophysical Chemistry Red Cabbage pH Indicator williams page

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    of Computational Chemistry School of Chemistry and Biochemistry MS E Building office 2100H Georgia Institute of Technology Atlanta GA 30332 0400 Tel 404 385 5169 email angelo bongiorno chemistry gatech

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