Harmonic force filed for amino acid L-glutamine by MNDO semiempirical method

Journalof Molecular Structure, 294 (1993) 49-52 Elsevier Science Publishers

B.V., Amsterdam

Harmonic force field for amino acid L-glutamine by MNDO semiempirical method J.T. Upez

Navatrete, J.J. Quit-ante and FJ. Ramirez

Departamentode QuimicaFlsica, Facultadde Ciencias.Universidadde Mdiaga,29071 -M&laga,SPAIN A scaled quadratic force field for amino acid glutamine has been calculated by using the semiempirical MNDO method. Scaled factors for a set of non-redundant local symmetry coordinates were transferred from glycine molecule and from the general behaviour of MNDO in vibrational frequencies calculations. The frequencies obtained compared favourably with the experimental ones; the descriptions of the normal modes confirmed the ~ignmen~

reported previously and some new ~i~rnen~

have been proposed.

med to a set of non-~dund~t

1. INTRODUCTION

local symmetry

coordinates defined following the Pulay description In a previous work [l] we reported the infrared

151.Frequencies and vibrations normal modes were

and polarized micro-Raman spectra of L-Glutamine

determined by the Wilson FG method [6]. The force

in the solid,

field was scaled on the diagonal

crystalline

~signment of the fu~en~s

state, and a general were proposed in the

basis of the relative intensity changes observed in

elements

by

transferring scaling factors from glycine molecule [4] and from data on MNDO systematic

vibrational

addition to isotopic shifts and correlations with data

frequency calculations [7]. All compu~tions

reported for related molecules. Glutamine is the more

performed

abundant free amino acid in human and mammalian

Physical Chemistry Department of tbe University of

blood and occupies an essential role in the nitrogen

Malaga.

metabolism

[2], therefore

the knowledge

were at the

of its

~bmtional spectra can be rather useful tool in many biological

in a p-VAX 2000 computer

3. RESULTS

AND DISCUSSION

studies. In order to progress in this

research work we report here a normal coordinate

The molecular structure of this amino acid in the

analyses of this amino acid based in the MNDG

solid state was determined by neutron diffraction [8]

semiempirical method [3], which was successly used

and X-ray difraction

elsewhere [4] to perform a force field calcu~tion for

demons~ated

amino acid glycine.

+H3N(COG-)CH(CH2)2CONH2. For this structure

tecniques

191, and they

that it occurs in zwiterionic

form,

the MNDG optimized geometrical parameters are 2. CALCULATIONS

close to the experimental ones, especially if we take into account the intermolecular hydrogen bonds that

To compute the force constants the molecular geometry of glutamine had to be optimized for a

stabilizes the crystal structure. The calculated values are very similar to the reported for amino acid

point of minimal energy. First and second derivatives

glycine by using the same method 141; the C-C and

of the SCF molecular energy were evaluated at this point and the initial Cartesian force field was transfor-

C-N bond lengths are slightlyt overestimated whereas C-H and C-O distances compare favourably. The

0022-2860/93/$06.000 1993 Elsevier Science Publishers B.V. All rights reserved.

50

able 1 Experimental and MNDO scaled fquencies (cm-‘) for L-glutamine molecule Vibsxtion

Calcul.

EXpZ

Diff.

P. E. D. (greater 10%)

Vl

3405

3403

2

V2

3302

3308

d

V3

3286

3280

6

V4

3208

3210

-2

Vs

3174

3176

-2

lOOV,(N Hz)

v6

2990

2991

99V&CH2)

V7

2965

-1 _

v8

2960

2%2

-2

72V,(CH& 29V,(CH2)

V9

2954

2952

2

VlO

2932

2933

-1

Vll

1686

1690

4

90V,(CH2), l0\$(CH2) 92v(C=O)

v12

1668

1645

23

57V(co,-),

h3

1604

1622

-18

63jj,(N H3+), 63v(C02-)

v14

1593

1604

-11

926,@H3+),

%J

1581

1590

-9

h6

1493

1496

-3

h7

1454

1449

5

7l&CH2),

v18

1409

1418

9

49V(C($-),

h9

1414

1415

1

33v’(CN), 28v(CO2-), 25v(CC)

V20

1379

v21

1363

1358

5

84&CH2) 61S(CH), 18V(CC), l6r(NH3’)

V22

1335

1330

5

45v(CC), 24r(N H3+), 16&CH)

v23

1307

1307

0

87WCH2)

v24

1286

1283

3

316UYCJQ

V25

1252

1256

-4

v26

1233

v21

1203

1202

1

v28

1158

1162

v29

1138

1130

8

v30

1118

1104

14

v31

1081

1094

-13

v32

1058

1052

6

37r(CH2), 25v(CC), ldj(CCN)

v33

993

loo0

-7

47V(CC), 12&N Hz)

v34

934

895

39

V35

853

849

4

v36

787

807

-20

77r(CH2), 14v(CN)

v37

750

776

-26

57y(oCCf, zO&ccc>

4

loov,(N4) lO2VJN H3+) lOOV,(NH3+) 98V,(N H3+)

6lV,(CH&

37V,(CH$

97v(CH)

546,(N H3+), 24&CCN) 17V(Co2-)

96&N H2) 1056,(NH3+) 53V(CC) 166(CH2), 14V’fcN)

79YCH2) 29&CH), 22V(CC), l8wCH2) 8OYCH2) 59r(N H3+), 376(CH) 7~H3+),

35&CH)

35&N I$), 2OWH2) 39&N Hz), 21V(CC)

Slv(CN), 36r(CH2), 15&CCN), 13v(CC) 78V(CC), 326(a2-)

51

‘Ihble 1 (Continued) vibration

Diff.

P. E. D. (greater 10%)

Calcul.

Exper.

V38

675

676

47&C($),

V39

642

653

34y(NCO), 166(CCN), 1ly(OCC), IO&CON H2)

v40

631

622

84’jIN H2), 28V’Wh

v41

578

604

236(CCNh 15&Co,-),

v42

556

560

47&CON H2). 31’y(N H2). lOv’(CN)

v43

473

452

5 1&CCN), 19&C@-)

v44

437

81&CONH2)

V45

370

432 _

v46

341

343

v47

320

V48

260

v49

184

184

0

93&(CCC)

v50

162

159

3

646(CCC), 262(CCC)

V51

85

84T(CCC), 246(CCC)

v52

50

632(C02-), 442(CCC)

v53

38

722(CCC), 5 lz(m,-)

v54

20

962(CCC)

21&CCN), 12&CCC)

%&CON

H2)

13y(NH2), 13V(CN), 1oy(NCo)

406(CCN), 4OT(NH3+), 24&C02-) 97W Hz), 12W Hz) 5 l&CCC), 38qCCN) l@‘WH3+)

Table 2 Force constants (in mdyn/A-l or mdyn-radlhi-2)and scaled factors obtained for L-glutamine Coord.

MNDO

WC) WC) WC023 WH)

Factor

scaled

Coord.

MNDO

Factor

scakd

6.266

1.oOO

6.266

2.798

1.400

3.917

3.707

1.140

4.226

1.061

1.117

1.185

16.14

0.685

11.06

0.409

1.046

0.428

5.761

0.842

4.85 1

0.768

0.785

0.603

wm

5.728

0.759

4.348

0.811

0.895

0.726

v,m3+1

7.237

0.727

5.261

0.858

1.031

0.885

6.49 1

0.878

5.699

17.80

0.603

10.73

6.114

0.8 14

4.977

9.040

0.859

7.765

v,C%)

5.633

0.848

4.777

7.444

0.772

5.747

ww

0.807

0.964

0.777

7.028

0.897

6.304

v,wJ3

+)

v,(CH2)

WH2)

1.038

0.950

0.986

1.061

1.000

1.061

&CH2)

0.866

0.824

0.714

0.570

1.000

0.570

cIyCH2)

0.792

0.996

0.789

0.735

0.773

0.568

t CH2)

0.664

1.013

0.673

0.813

1.000

0.813

&CCC)

1.667

0.804

1.340

52

bond angles are calculated in good accord with the

constant smaller than the others C-C coordinates,

observed values even for angles involving polar

4.226 and

6.266 mdyn/A respectively;

the bond

groups such as the ‘H3N, COO- or amide moieties.

orders calculated by MNDQ, namely 0.678 and 0.969

The mean absolute errors were 0.023A for bond

respectively, confirm these results. The comparison

lengths and 2.25 degrees for bond angles.

between force constants and bond orders is in the

The results of the normal coordinate calculation

same way for the two C-N stretching modes: from

are summarized in Tables 1 and 2. The former shows

amonium and amide groups; the smaller value for the

calculated and observed frequencies in addition to the

former,

description of the vibrations by means the potential

corresponding bond order of 0.846, whereas for the

energy distribution. The frequencies higher than 1000

C-NH2 the values are 7.765 mdyn/A and 1.046

cm-l

are calculated with minimal errors and the

respectively. The v(NH) modes are similar force

corresponding assignments are in good accord with

constants both in the amonium and amide group.

the proposed elsewhere [ 11; greater differences result

Finally, the force constants for bending modes are in

for v(CO2-) and &,(NHs+) modes (~12 - v14

general lower than 1.5 mdyn/A except for the

frequencies)

G(CCN) coordinate, in accord with data reported for

because there is a lot of coupling

4.348 mdyn/A,

between them. We would like to emphasize that the

glycine

assignments obtained for the characteristical amide

molecule

calculations.

is in accord

[l] by different

with the

force

field

vibrations, named Amide I, II and III, have confirmed the reported

previously

[l] in the basis of the

intensity changes observed from the polarized microRaman spectra of solid glutamine.

REFERENCES

Some new

assignments have been proposed in the present work

P.Dhamelincourt and F_J.Ramfrez, Appl.

for the

Spectrosc. (in press)

1000-200

cm-l

region;

however

the

frequencies in this zone can not be assigned to single

R.Palacios and J.Mora, Glutamine: Metabolism,

vibrations

Enzymology and Regulation, Academic Press,

because they usually involve several

internal coordinates.

New York, 1980.

Table 2 summarizes the diagonal force constants

M.J.S.Dewar and W. Thiel, J. Am. Chem. Sot.,

and the scaling factors obtained for the internal

99 (1977) 4899.

coordinates of glutamine molecule. Force constants

J.T.L@ezNavarrete, J.J.Quirante and

related to modes with the same character were

F.J. Ramfrez, J. Mol. Struct., 268 (1992) 249.

averaged and torsional modes were not scaled because

P.Pulay, G.Fogarasi, EPang and J.EBoggs,

the corresponding frequencies are very sensitive to

J. Am. Chem. Sot., 101 (1979) 2550.

the three-dimensinal

network of hydrogen bonds

E.B.Wilson, J. Chem. Phys., 99 (1939) 1047.

which exists in the solid state, unlike in the

M.J.S.Dewar, G.PFord, M.L.McKee, HRzepa,

individual molecule. The scaled values have corrected

W.Thiel and Y.Yamaguchi, J. Mol. Struct., 43

the systematical errors from the MNDG method and

(1978) 135.

they are in gocxl accord with the zwiterionic structure

8

of this amino acid. The highest values correspond to the CO2- stretching coordinates and this explains

T. EKoetzle, M.N.Frey, M.S.Lehmann and W.C.Hamilton, Acta Cryst., B29 (1973) 2571.

9

W.Cochran and B.R.Penford, Acta Cryst., 99

that

the Co- CO2- stretching mode had a force

(1952) 644.