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Salt Bridge Structures in the Absence of Solvent? The Case for the Oligoglycines
Thomas Wyttenbach, John E. Bushnell, and Michael T. Bowers
J. Am. Chem. Soc. 1998, 120, 5098-5103

    1. B3LYP geometries for GlyNa+, GlynNa+, n =1 - 4. Cartesian coordinates and energies for 2 GlyNa+, 3 Gly2Na+, 4 Gly3Na+ and 2 Gly4Na+ isomers.
    2. Frequencies (B3LYP) for GlyNa+ and Gly2Na+.
    3. Molecular mechanics geometries for Gly5H+ and Gly5Na+. Cartesian coordinates of structures shown in Figure 4.

 

A. B3LYP Geometries for GlynNa+, n = 1- 4. Cartesian Coordinates in Å.

 

GlyNa+ Basis Set: 6-311++G**

------------------------------------------------

Struct. 1-1 (for 6-311G frequencies see sectn B) Energy: 0.00 kcal/mol

11

C -1.308226 0.171267 0.000000

C 0.000000 0.945860 0.000000

O -0.208671 2.251312 0.000000

H 0.639257 2.726358 0.000000

O 1.109599 0.441095 0.000000

N -1.097214 -1.291440 0.000000

Na 1.323539 -1.774665 0.000000

H -1.557798 -1.702474 0.807060

H -1.557798 -1.702474 -0.807060

H -1.880076 0.498980 -0.872241

H -1.880076 0.498980 0.872241

------------------------------------------------

Struct.1-2 (for 6-311G frequencies see sectn B) Energy: 2.75 kcal/mol

11

C -1.495841 .720464 .000016

C -.007100 .312579 .000005

O .846188 1.207863 .000034

O .206097 -.941182 -.000026

N -2.284782 -.570411 -.000016

H -2.870505 -.688149 -.827583

Na 2.482962 -.389254 -.000006

H -2.870506 -.688189 .827543

H -1.506084 -1.288707 -.000036

H -1.736322 1.304029 -.886611

H -1.736321 1.303981 .886675

------------------------------------------------

Gly2Na+ Basis Set: 6-311++G**

------------------------------------------------

Struct. 2-1 (for 6-31G frequencies see sectn B) Energy: 0.00 kcal/mol

18

H -3.552295 -1.198783 -1.273440

N -3.211694 -.946649 -.354153

H -3.971916 -1.069513 .303304

C -2.649645 .401512 -.314091

H -3.192900 1.067653 .362956

H -2.671306 .885474 -1.294737

C -1.195012 .419049 .151319

O -.572023 1.484854 .267789

N -.667123 -.786060 .417747

H -1.311323 -1.563796 .275530

C .645024 -.990689 1.010431

H .683735 -1.994947 1.428263

H .806870 -.264861 1.810595

C 1.767534 -.819541 -.013330

O 2.218426 .259149 -.359506

O 2.198842 -1.973965 -.497667

H 2.902124 -1.816929 -1.150697

Na 1.389942 2.351125 -.108894

------------------------------------------------

Struct. 2-2 Energy: 1.25 kcal/mol

18

C -.895896 -.835518 .307107

O -.725954 -.108243 1.286159

N .128878 -1.490750 -.280882

H -.036201 -2.022400 -1.122605

C 1.497642 -1.262193 .135010

H 2.155985 -1.984357 -.347528

H 1.598358 -1.399532 1.215507

C 1.980919 .151878 -.183728

O 1.272633 1.082137 -.519606

O 3.293173 .246334 -.020412

H 3.586304 1.156290 -.192678

Na -.813117 1.896570 .121756

C -2.271599 -.926593 -.345845

N -2.840612 .443321 -.365346

H -2.199540 -1.299627 -1.368879

H -2.883698 -1.634346 .223552

H -3.392248 .592712 .475506

H -3.487738 .533736 -1.142983

------------------------------------------------

Struct. 2-3 (for 6-31G frequencies see sectn B) Energy: 13.70 kcal/mol

18

N -1.284290 1.857162 0.262652

H -1.728847 2.134182 -0.616913

H -1.274880 2.663261 0.888477

H -0.272693 1.495204 0.072639

C -2.019366 0.684877 0.851075

H -3.049484 0.965187 1.060097

H -1.511311 0.407183 1.772338

C -2.032191 -0.386511 -0.250105

O -2.852085 -0.274409 -1.143282

N -1.094437 -1.365932 -0.204385

H -1.145910 -2.000452 -0.992784

C 0.095139 -1.457576 0.632933

H -0.148882 -1.252151 1.679257

H 0.456242 -2.483376 0.596722

C 1.262870 -0.537368 0.221915

O 1.027617 0.700446 -0.070929

O 2.404186 -1.018262 0.214430

Na 3.350036 0.868147 -0.509487

------------------------------------------------

Gly3Na+ Basis Set: 6-31G

------------------------------------------------

Energy: 0.00 kcal/mol

25

O -0.531200 -2.018200 -4.082100

C -0.383000 -1.508800 -2.840500

H 0.314600 -2.309700 -4.490100

C -1.708400 -0.999600 -2.300600

O 0.714900 -1.434700 -2.263200

N -1.765300 -0.963300 -0.845300

H -2.514700 -1.624200 -2.686800

H -1.851000 0.012900 -2.700800

C -1.132500 0.000500 -0.119100

H -2.303000 -1.679100 -0.375400

NA 1.717700 -0.070600 -0.804700

C -1.316800 -0.101600 1.399400

O -0.419700 0.876100 -0.671200

N -0.465200 0.792900 2.153200

H -1.130400 -1.143300 1.697200

H -2.358000 0.128100 1.648700

C 0.878000 0.794000 2.106400

H -0.841000 1.485300 2.806500

C 1.545100 1.785100 3.060000

O 1.565200 0.044100 1.348200

N 0.570100 2.565800 3.819500

H 2.203700 2.422900 2.457900

H 2.202000 1.202700 3.717100

H 0.521100 3.550800 3.592700

H 0.557600 2.404100 4.818400

------------------------------------------------

Energy: 0.03 kcal/mol

25

H -4.953053 -0.221558 -1.018136

N -4.017661 -0.416022 -1.353638

H -4.016201 -0.679742 -2.330654

C -3.188475 -1.237378 -0.471928

H -2.716177 -2.063512 -1.016975

H -3.767502 -1.699987 0.336851

C -2.075024 -0.428154 0.186926

O -1.280634 -0.945728 1.025338

N -2.000967 0.863591 -0.196891

H -2.741850 1.138898 -0.845666

C -1.110759 1.823520 0.453412

H -1.355464 1.928834 1.514461

H -1.242987 2.796626 -0.028624

C 0.361873 1.406468 0.395822

O 1.035516 1.248872 1.449151

N 0.905662 1.204069 -0.832648

H 0.322527 1.289134 -1.653862

C 2.315427 0.880161 -1.014185

H 2.924687 1.531872 -0.373920

H 2.605645 1.069296 -2.048313

C 2.674573 -0.550798 -0.652876

O 2.075998 -1.274145 0.158872

O 3.796950 -0.938313 -1.299822

H 4.104131 -1.836404 -1.043289

Na 0.703516 -0.991212 1.921729

------------------------------------------------

Energy: 3.72 kcal/mol

25

N 2.722935 -1.016038 0.035295

H 3.574395 -1.462870 -0.303726

H 2.572688 -1.254214 1.016599

H 1.517992 -1.543318 -0.688002

C 2.753983 0.463366 -0.156222

H 2.974941 0.670076 -1.205921

H 3.528923 0.940490 0.458162

C 1.389580 1.009751 0.248379

O 0.826912 0.564243 1.286322

N 0.791971 1.917197 -0.564071

H 1.293263 2.275761 -1.365197

C -0.606126 2.348851 -0.351304

H -0.717877 2.868884 0.601866

H -0.879346 3.030017 -1.160842

C -1.507856 1.102723 -0.308851

O -2.108577 0.778640 0.748487

N -1.481850 0.302520 -1.406017

H -0.972122 0.603180 -2.225667

C -1.750077 -1.148259 -1.296808

H -1.834665 -1.569467 -2.298251

H -2.667367 -1.321806 -0.736965

C -0.540932 -1.718027 -0.548170

O -0.601001 -2.063727 0.656142

O 0.585044 -1.614655 -1.247912

Na -0.970244 -0.484447 2.216822

------------------------------------------------

Energy:15.56 kcal/mol

25

N -2.075700 -1.802300 -0.853900

H -1.044500 -1.897500 0.077600

C -2.913600 -0.552800 -0.700800

H -1.636600 -1.860500 -1.774000

H -2.651100 -2.636800 -0.724500

H -3.336500 -0.257000 -1.667100

H -3.731900 -0.775600 -0.016100

C -2.107300 0.576700 -0.059800

O -2.134000 0.763900 1.176700

N -1.304600 1.321500 -0.885200

H -1.353600 1.219000 -1.888900

C -0.348100 2.301600 -0.326700

H -0.037300 2.990300 -1.110600

H -0.831400 2.857100 0.480600

C 0.860600 1.500900 0.163200

O 1.861200 1.306800 -0.590700

N 0.696300 0.872200 1.349800

Na 3.061000 -0.346600 -1.327900

H -0.197500 0.998800 1.822800

C 1.452800 -0.350500 1.687400

H 2.526500 -0.178700 1.608000

H 1.203600 -0.642500 2.706700

C 0.961500 -1.398300 0.677500

O 1.644500 -1.698800 -0.342200

O -0.275300 -1.773000 0.902800

------------------------------------------------

Gly4Na+ Basis Set: 6-31G

------------------------------------------------

Energy: 0.00 kcal/mol

32

H 4.966745 -.739871 -2.230038

N 4.856768 -.949127 -1.246152

H 5.722467 -1.269631 -.830112

C 3.662810 -1.717692 -.890453

H 3.075342 -1.978321 -1.778884

H 3.906469 -2.666454 -.396783

C 2.739509 -.949906 .051917

O 1.688314 -1.471225 .519799

N 3.134229 .310940 .333775

H 4.029242 .562162 -.090142

C 2.454639 1.146430 1.321553

H 2.419710 .646264 2.293674

H 3.018614 2.077406 1.429336

C 1.001916 1.446714 .945100

O .042035 1.029285 1.648115

N .773835 2.158014 -.188340

H 1.543093 2.407532 -.792616

C -.589681 2.414550 -.634178

H -.544492 2.964266 -1.579441

H -1.110094 3.041788 .098547

C -1.370203 1.112233 -.852132

O -.798471 .030748 -1.135890

N -2.721844 1.202063 -.734577

H -3.144299 2.061877 -.412712

C -3.600060 .075448 -1.021670

H -4.615163 .435323 -1.192735

H -3.263046 -.423514 -1.939554

C -3.627800 -.981275 .070119

O -2.704713 -1.252650 .851774

O -4.801813 -1.656162 .050434

H -4.836215 -2.388936 .705055

Na -.445352 -1.136554 .922552

------------------------------------------------

Energy: 4.86 kcal/mol

32

N -3.044027 -1.510226 -.056103

H -3.829392 -2.126776 -.257655

H -2.844537 -1.495537 .946855

H -1.780647 -2.061901 -.601115

C -3.253509 -.138497 -.573691

H -3.257571 -.167425 -1.667623

H -4.214509 .285610 -.246811

C -2.134983 .755683 -.052420

O -1.553479 .483235 1.029163

N -1.811959 1.851370 -.788317

H -2.314762 2.046202 -1.643284

C -.856311 2.856989 -.289307

H -.793389 3.657263 -1.031325

H -1.207149 3.278676 .655733

C .527282 2.253600 -.004052

O .938894 2.126175 1.172773

N 1.250757 1.829035 -1.079728

H .892799 1.976187 -2.012778

C 2.561451 1.162783 -.929000

H 3.040360 1.127347 -1.910181

H 3.186890 1.737590 -.243354

C 2.367703 -.230544 -.320629

O 2.407652 -.394774 .925778

N 2.028271 -1.247817 -1.154821

H 2.004160 -1.115462 -2.155628

C 1.563697 -2.536583 -.603582

H 1.555276 -3.275862 -1.403873

H 2.233929 -2.849141 .197721

C .155286 -2.341777 -.043274

O -.059706 -2.102264 1.170045

O -.793688 -2.340698 -.976385

Na .478741 -.030602 2.113712

------------------------------------------------

 

B. Frequencies for GlyNa+ (B3LYP/6-311G) and Gly2Na+ (B3LYP/6-31G). Vibrational Frequencies in cm-1.

 

GlyNa+ structure 1-1

55 99 206 265 342 454 494 526 653 691 857 946 995 1116 1147 1237 1353 1383 1456 1502 1680 1744 3050 3092 3475 3556 3631

structure 1-2

92 122 143 274 296 366 527 562 700 881 944 948 1131 1171 1321 1332 1364 1513 1527 1650 1710 1732 2837 3102 3162 3463 3532

 

Gly2Na+ structure 2-1

37 67 102 116 147 191 227 240 288 311 345 421 533 561 585 636 703 754 789 857 896 906 943 1047 1107 1117 1168 1204 1284 1308 1368 1390 1398 1440 1502 1513 1585 1664 1712 1722 3061 3084 3107 3181 3419 3568 3582 3674

structure 2-3

48 52 84 129 143 247 259 286 318 345 441 463 499 548 621 691 749 788 815 907 938 961 1011 1119 1149 1191 1283 1331 1356 1379 1409 1460 1498 1516 1539 1578 1649 1689 1730 1738 2257 3071 3136 3168 3205 3432 3522 3591

 

 

C. Molecular Mechanics Geometries for Gly5H+and Gly5Na+. Cartesian Coordinates in Å.

 

Gly5Na+ structure shown in Figure4a

------------------------------------------------

39

H -4.639481 -3.032761 2.765961

N -4.322784 -2.782867 1.838623

H -4.620972 -3.345703 1.053436

C -3.061874 -2.070572 1.719696

H -2.239288 -2.769531 1.876465

H -3.013443 -1.290985 2.481033

C -2.938293 -1.432770 0.336960

O -1.940964 -1.629944 -0.360077

N -3.969009 -0.685791 -0.066391

H -4.759338 -0.591324 0.554916

C -4.036102 -0.034378 -1.367400

H -4.930008 0.589218 -1.416550

H -4.097855 -0.794006 -2.147827

C -2.799423 0.829941 -1.591995

O -1.921570 0.467667 -2.378128

N -2.689850 1.932877 -0.850845

H -3.426849 2.154739 -0.198700

C -1.546219 2.832352 -0.921951

H -1.690200 3.642212 -0.206360

H -1.493988 3.256989 -1.926315

C -0.229736 2.119095 -0.604600

O -0.224243 0.972687 -0.142441

N 0.894577 2.784210 -0.875671

H 0.824219 3.703644 -1.285187

C 2.229584 2.246078 -0.649918

H 2.368912 2.083069 0.419449

H 2.965073 2.975845 -0.993118

C 2.454254 0.929520 -1.397629

O 1.624786 0.513321 -2.210648

N 3.558075 0.244354 -1.101837

H 4.203949 0.624817 -0.425934

C 3.872086 -1.048920 -1.691208

H 4.930023 -1.261795 -1.527740

H 3.687607 -1.032242 -2.765976

C 3.029984 -2.150055 -1.047409

O 1.798859 -2.064270 -1.100952

O 3.672028 -3.068802 -0.281891

H 3.064194 -3.703629 0.101120

Na -0.154861 -0.893800 -1.678207

------------------------------------------------

Gly5Na+ structure shown in Figure 4b

------------------------------------------------

39

N -0.590805 2.384216 -0.569138

H -0.055084 2.602737 0.269211

H -0.353424 3.029846 -1.303558

H -0.251175 1.467728 -0.854004

C -2.020569 2.306198 -0.251923

H -2.562973 1.920746 -1.115662

H -2.394089 3.299377 -0.001526

C -2.190521 1.390015 0.952850

O -1.468765 1.558990 1.934891

N -3.079056 0.393265 0.882355

H -3.654739 0.288269 0.060577

C -3.098236 -0.678909 1.871368

H -3.881119 -1.398254 1.627594

H -3.289703 -0.269592 2.864304

C -1.730759 -1.356735 1.838135

O -0.871231 -1.067612 2.671387

N -1.498810 -2.150848 0.794983

H -2.253418 -2.322983 0.148743

C -0.156219 -2.450760 0.321884

H -0.166107 -3.433594 -0.150314

H 0.568268 -2.460281 1.138260

C 0.242371 -1.393753 -0.709152

O -0.413254 -0.347137 -0.812256

N 1.272537 -1.687805 -1.507462

H 1.765686 -2.554474 -1.356400

C 1.771347 -0.793579 -2.544250

H 1.019547 -0.688416 -3.327057

H 2.682693 -1.205078 -2.979919

C 2.065704 0.567108 -1.926529

O 1.321472 1.524109 -2.145462

N 3.078384 0.618057 -1.065506

H 3.588211 -0.229828 -0.875244

C 3.151627 1.645157 -0.047379

H 3.017242 2.639236 -0.477829

H 4.117400 1.596146 0.456894

C 2.041229 1.324951 0.943619

O 1.239395 2.210876 1.307922

O 1.887543 0.144943 1.316437

Na 0.535721 0.764053 2.982422

------------------------------------------------

Gly5H+ structure shown in Figure 4c

------------------------------------------------

39

N 0.021637 -1.781525 0.824585

H 0.499390 -2.540207 1.276474

H -0.073196 -0.996750 1.465164

H 0.611800 -1.416687 0.080124

C -1.300461 -2.137405 0.298660

H -1.863770 -2.655838 1.075241

H -1.199295 -2.791595 -0.567917

C -2.035751 -0.855377 -0.063980

O -2.633377 -0.234680 0.807129

N -1.931366 -0.406479 -1.314346

H -1.356613 -0.907333 -1.976730

C -2.342178 0.942749 -1.668396

H -3.356140 1.150208 -1.321487

H -2.310013 1.056473 -2.752518

C -1.339722 1.894700 -1.026184

O -0.276505 2.132828 -1.597626

N -1.611100 2.342621 0.196976

H -2.436844 1.982025 0.657990

C -0.597534 2.981842 1.019012

H -1.050537 3.332932 1.946274

H -0.168991 3.832703 0.485947

C 0.480148 1.948532 1.346024

O 0.165787 0.768158 1.514984

N 1.748108 2.362869 1.404083

H 1.948105 3.340668 1.253189

C 2.862778 1.462646 1.674103

H 2.741684 1.026000 2.666794

H 3.798767 2.021912 1.650513

C 2.899292 0.349411 0.628357

O 2.478287 -0.776611 0.891739

N 3.339951 0.674896 -0.585495

H 3.658737 1.616302 -0.758209

C 3.229477 -0.230911 -1.716995

H 3.493027 -1.250778 -1.430359

H 3.906189 0.093872 -2.508362

C 1.792862 -0.184509 -2.222839

O 0.921967 -0.760880 -1.560364

O 1.513763 0.801071 -3.113922

H 0.727112 1.293976 -2.855835

------------------------------------------------

 

    

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