Conformational study on dipeptides containing phenylalanine: A DFT approach

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Journal of Molecular Structure: THEOCHEM 810 (2007) 81–89

Conformational study on dipeptides containingphenylalanine: A DFT approach

Souvik Mondal, Durga Sankar Chowdhuri, Soumen Ghosh, Ajay Misra, Sudipta Dalai *

Department of Chemistry and Chemical Technology Vidyasagar University, Midnapore, 721102 W.B, India

Received 8 December 2006; received in revised form 2 February 2007; accepted 5 February 2007Available online 13 February 2007

Abstract

DFT calculations has been done applying 6-31G* basis set on a series of dipeptides where the N-terminus position is fixed with phen-

ylalanine and the C-terminus is varied with eight different amino acids. Different geometrical parameters (bond angle, bond length, geom-etry around a-carbon atom) are thoroughly investigated to study the effect of amino acid sequence on dipeptide. Dihedral angle dataanalysis shows the deviation of amide plane from planarity, which is due to the combined effect of the steric hindrance of –R groupand hydrogen bonding. The kmax value for phenylalanine has been calculated, which shows good agreement with the experimental value.A rigid potential energy scan is performed on phenylalanine by rotating –CH2Ph, –COOH and –NH2 groups separately to get some ideaabout the conformational stability.� 2007 Elsevier B.V. All rights reserved.

Keywords: Phenylalanine; Dipeptide; Peptide bond; DFT calculation; Potential energy scan

1. Introduction

Proteins are a relatively homogeneous class of mole-cules built of twenty naturally occurring amino acids.Proteins are used for regulatory roles, monitoringextracellular and intracellular conditions and relayinginformation to other cellular components. In additionto this, they are essential structural component of cell.In fact every property that characterizes a living organ-ism is affected by protein [1]. The keys to realize thefunction of a given protein is to understand its structure.The proteins are the polymers of smaller units (aminoacid) like the other biological molecules like nucleicacids, polysaccharides. But the difference lies in the factthat unlike any nucleic acids, proteins are not confinedto uniform, regular structure. This is due to the fact thatthe all twenty amino acid residues from which proteins

0166-1280/$ - see front matter � 2007 Elsevier B.V. All rights reserved.

doi:10.1016/j.theochem.2007.02.006

* Corresponding author. Fax: +91 3222 275329.E-mail address: [email protected] (S. Dalai).

are made, differ in physical and chemical properties[2,3]. So the function of protein is controlled by its threedimensional structure which is dependent on the linearsequence of amino acids in the protein [3]. The predic-tion of 3D structure of a protein from the knowledgeof linear sequence of amino acids has been describedas determination of the second half of the genetic code[4]. The process of generating three dimensional structureof protein from the primary structure is an interestingtopic to reveal several interesting facts of protein folding[5].

Peptides and proteins are basically the polymers ofamino acids. Two amino acids joined by a peptide bondis called a dipeptide, similarly, when a few amino acidsare joined in the same fashion the structure is called oligo-peptide. Polypeptides are formed when many amino acidsare linked. Peptides are formed by highly controlled poly-merization reaction and the polymerization is based onthe formation of the amide bond, usually called the peptidebond.

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82 S. Mondal et al. / Journal of Molecular Structure: THEOCHEM 810 (2007) 81–89

RC

O

NH

R '

The amide plane

Ab initio calculation on peptide structures has beendone [6]. Previous theoretical works [7–18] on rigid geom-etries of the dipeptides and diamides were not sufficient[19–28] due to less advancement of technology at that per-iod of time. Recent papers [29–35] have made some inves-tigation on the structure of diamides, dipeptides and othershort chain peptides. Our group has also published a paperon the structural investigation of peptide [36]. These stud-ied have limited the potential energy to functions of onlythe torsion angles within the amino acid residues by wayof the Ramachandran plot [37,38].

During the conformational study, even a simple mole-cule might be considered to exist in an infinite number ofconformations if the positions of the atoms are definedwith sufficient accuracy because bond lengths and bondangles vary at room temperature by ±0.5 A and ±5�,

Fig. 1. Energy optimized structu

respectively due to thermal vibration. For this reason, onlythe energetically most stable arrangement i.e. energy min-ima that are separated by distinct energy barriers are usu-ally classified as individual conformation. In the presentwork, we did an extensive theoretical study on eight differ-ent dipeptides using DFT-B3LYP/6-31G* level of theory.A thorough investigation on the geometry around the a-carbon atom, the dihedral angles of the amide plane, thebond angles and the bond lengths of the amide plane indipeptide structures are carried out in the present article.The kmax value for phenylalanine has been calculated,showing good agreement with the experimental value. APES study has been performed on phenylalanine by rotat-ing –CH2Ph, –COOH and –NH2 group to get the lowenergy conformations.

2. Computational details

The eight dipeptide structures studied were optimized atDFT level individually. The density functional methodadopted here is B3LYP i.e. Becke’s three parameter hybridfunctional using Lee–Yang–Parr [39] correlation function.The minima of the geometries are located using 6-31G*basis set in each case. The energy minimized structures ofeight dipeptides at DFT-B3LYP/6-31G* level is shown in

re of the dipeptides studied.

Fig. 1 (continued)

S. Mondal et al. / Journal of Molecular Structure: THEOCHEM 810 (2007) 81–89 83

Fig. 1. All the computations have been done applyingGaussian 03 program [40].

The generalized geometrical scheme with the atom num-bering is given in Fig. 2. Atom 26C is the first atom of the –R group. u is the dihedral angle between atom 7C and 27Cabout 22N–24C bond. Atom 4C and 24C are the a-carbon

Fig. 2. Geometrical scheme with the atom numbering of the dipeptidesstudied.

atoms. The optimized energies of the dipeptides are listedin Table 1.

The eight dipeptides were constructed with differentcombinations where phenylalanine is fixed at the N-termi-nus position. The C-terminus position is named as A-posi-tion. In these dipeptides the A-position is varied withdifferent amino acids which are connected to the fixed phen-

ylalanine end at N-terminus position. Eight different aminoacids are chosen for A-position and they are asparagine

(Asn), aspartate (Asp), cystine (Cys), glycine (Gly), valine(Val), serine (Ser), tyrosine (Tyr) and phenylalanine

(Phe). All these are taken as neutral species. The structuralparameters were analyzed after optimization of all thedipeptide molecules at DFT level with B3LYP correlation

Table 1Calculated energy (kJ mol�1) of the eight dipeptides studied

Dipeptide combination DFT-B3LYP/6-31G*

Phe–Asn �2549220Phe–Asp �2601382Phe–Ser �2303720Phe–Cys �3151817Phe–Gly �2003004Phe–Tyr �2910457Phe–Val �2312715Phe–Phe �2712957


function applying 6-31G* basis set. The atom-numberingscheme is given in Fig. 2. This atom numbering scheme willbe referred throughout this paper wherever necessary.

3. Results and discussion

3.1. Bond length and bond angle

Five bond lengths (in A) for the amide planes wereconsidered for eight combinations and those are 4C–7C,7C–11O, 7C–22N, 22N–24C and 22N–23H all of whichare listed in Table 2 with particular atom numbering as

Table 2Bond length (A) [calculated] for amide plane for all combination of dipeptide

A-amino acids C(4)–C(7) C(7)–O(11)

Asn 1.539 1.229Asp 1.540 1.226Ser 1.538 1.230Cysa 1.538 1.230Gly 1.539 1.228Tyr 1.541 1.227Val 1.533 1.231Phe 1.537 1.232Average 1.538 1.229Maximum deviation 0.005 0.003

a For Cys: N(22)–C(24) will be N(22)–C(23).

Table 3Bond angles (�) [calculated] for amide plane for all combination of dipeptides

Dipeptide combination \CCO (4-7-11) \CCN (4-7-22) \OCN (1

Phe–Asn 120.87 116.40 122.72Phe–Asp 121.02 115.84 123.13Phe–Ser 120.88 116.44 122.66Phe–Cysa 120.98 116.53 122.46Phe–Gly 120.87 116.15 122.96Phe–Tyr 120.75 115.96 122.72Phe–Val 120.50 116.54 122.95Phe–Phe 120.84 116.70 122.43Average 120.83 116.32 122.82Maximum deviation 0.33 0.48 0.45

a For Phe–Cys dipeptide combination: C(24) will be C(23) and H(23) will b

Table 4Calculated a-carbon bond angles (�) in both amino acid residues of the eight

A-amino acid Bond angles (�)

Phenylalanine

\CCaN (6-4-1) \CCaH (6-4-5) \CCa plane (6-4

Asn 108.66 108.54 109.54Asp 108.68 108.57 109.40Ser 108.64 108.74 109.48Cysa 108.71 108.75 109.46Gly 108.74 108.54 109.65Tyr 108.62 108.55 109.59Val 114.26 108.64 109.38Phe 108.70 108.77 109.55Average 109.37 108.63 109.50Maximun deviation 4.89 0.14 0.15

a For Phe–Cys dipeptide combination: C(24), H(23), C(26) and C(25) will b

indicated in Fig. 2. It is observed on studying the five bondlengths (mentioned earlier) of the amide plane of eightdipeptides that the maximum deviation in bond length isonly 0.009 A, indicating a very little change in bond lengthwith changing A-group in dipeptides with different aminoacids.

Six bond angles (in �) related to amide plane were inves-tigated; those are \CCO (4-7-11), \CCN (4-7-22), \OCN(11-7-22), \CNC (7-22-24), \CNH (7-22-23) and \HNC(23-22-24), listed in Table 3 with respect to atom number-ing (Fig. 2). The maximum deviation of bond angle ofamide plane is 0.63� with the exception of bond angle devi-

s studied

C(7)–N(22) N(22)–C(24) N(22)–H(23)

1.362 1.461 1.0121.370 1.455 1.0121.361 1.453 1.0121.361 1.452 1.0131.364 1.444 1.0101.367 1.460 1.0111.355 1.454 1.0121.358 1.452 1.0121.362 1.453 1.0120.008 0.009 0.002

studied

1-7-22) \CNC (7-22-24) \CNH (7-22-23) \HNC (23-22-24)

122.38 120.00 117.16121.82 118.25 116.53122.17 120.85 116.13121.83 120.89 115.86121.99 119.10 118.44122.58 118.35 116.83122.00 120.94 116.54121.39 121.19 116.49122.02 119.94 116.74

0.63 1.69 1.7

e H(34).

dipeptides studied

A-amino acids

-7) \RCaC (26-24-27) \RCaH (26-24-25) \RCa plane (26-24-22)

111.32 110.15 110.76110.87 109.01 111.19110.54 108.63 110.15112.30 108.20 110.05106.68 106.72 111.91112.35 110.32 111.31113.01 107.59 111.97111.56 108.17 111.32111.07 108.59 111.08

4.39 1.87 1.03

e C(23), H(34), C(25) and C(24), respectively.

Table 5Dihedral angles (�) [calculated] of the amide plane for the dipeptidesstudied

A-amino acid Dihedral angles (�)

D1 (180) D2 (180) D3 (0) D (180)

Asn 179.83 �174.18 �2.07 �172.10Asp 179.98 �168.86 �10.36 �158.49Ser �179.44 �174.06 �4.90 �169.15Cysa �179.17 �173.08 �7.19 �18.71Gly 179.78 �176.26 �4.15 �172.11Tyr �179.67 �171.11 �8.59 �162.52Val �179.98 �176.02 �4.35 �171.66Phe �179.19 �175.14 �6.42 �168.71

a For Cys: C(24) will be C(23).


ation of \CNH (7-22-23) and \HNC (23-22-24) with 1.69�and 1.7�, respectively. This may be due to the variation inthe –R group of the amino acids connected to phenylalanine

i.e. A-group.It is clear that the very little difference in bond length

and bond angle with the variation of A-group is probablydue to the steric interaction of local species or thosedirectly bonded to the atom which is connected to thea-carbon atom and H-bonding (discussed in Section 3.3).

3.2. a-carbon geometry

For peptide structure the geometry around a-carbonatom plays very important role in the overall structureof protein if they vary significantly throughout a seriesof amino acid residues. Slight deviation should have abig impact as the protein consists of thousands of resi-dues. Ideally bond angle around carbon atom is 109.5�.But due to the streogenic nature of a-C atom the idealnature is not expected. In this part the emphasis willbe on how the bond angle around a-carbon changeswhen the A-group amino acid is changed with Asn,

Asp, Ser, Cys, Gly, Tyr, Val and Phe. Appreciablechanges in the angles would suggest that the same geom-etry is not retained by a-carbons and should be consid-ered in larger protein structure prediction. The bondangles were measured for both the residues of eightdipeptides i.e. for fixed amino acid residue and varyingresidue (A-group) for each combination. Each dipeptidesstudied in the paper have two a-C centers, C-4 and C-24(shown in Fig. 2). Therefore a-carbon bond angle studiedhere are \CCaN (6-4-1), \CCaH (6-4-5), \CCa plane(6-4-7), \RCaC (26-24-27), \RCaH (26-24-25) and\RCa plane (26-24-22). The angles formed between thefirst atom of the –R group and each of the other threesubstituents on a-carbon were examined. a-carbon bondangles (�) are given in Table 4. The left portion of thetable contained the phenylalanine residues of the dipep-tides which remained fixed at the N-terminus positionall along the whole study and the right side of Table 4has the A-amino acid residues. The range of angles forphenylalanine residue is not very large. Therefore thegeometry around a-C atom (4C) does not change verymuch with the variation of A-group. This is due to thefact that the bulkiness of the –R group of the amino acidresidues (A-group) have a little effect as this resides in adistance. But the geometry around a-C atom (24C) ofthe A-group does vary, which is reflected specially inthe bond angle of \RCaC (26-24-27). This is becausethe varying –R group is in the nearest position and havean impact on the bond angle around 24C. All the dataare listed in Table 4 suggest that the geometry arounda-carbon atoms are not retained throughout an aminoacid sequence, so this factor must be taken into accountfor consideration in case of larger peptides.

Another interesting fact in Table 3 is the geometry of thetwo phenylalanine a-C atoms, when both of them are

present in Phe–Phe combination. This comparison revealsdifferences in bond angles about the a-carbon atoms ofthe two positions in the dipeptide in spite of the fact thatboth positions are occupied by the same amino acid resi-due. This difference can be explained by the fact that thereis a significant difference between the N of the amine groupfor the first amino acid and the N of the plane (previouslyof amine group) of the A-amino acid and similarly with thecarboxyl carbon.

3.3. Dihedral angle

Planarity of the amide plane and information aboutpeptide bond are the key factors for investigation of thepeptide molecules. Dihedral angle of the dipeptide bondcan supply that information. The dihedral angle betweenatoms 24C and 23H with respect to atoms 7C and 22N[peptide bond: 7C–22N] is important for considerationand will be named as ‘D’. The dihedral angle ‘D’ shouldbe 180� if the amide plane is planar. The other importantdihedral angles which supply valuable information aboutthe planarity of the peptide bond are: (i) the angle betweenatoms 22N and 11O with respect to the bond joining 4Cand 7C referred as ‘D1’ (ii) the angle between atoms 4Cand 24C with respect to the bond joining atoms 22N and7C i.e. the peptide bond, referred as ‘D2’ (iii) the anglebetween atoms 4C and 23H with respect to the peptidebond i.e. the bond joining atoms 22N and 7C, referred toas ‘D3’. For a planar structure all the above said dihedralangles should be 180�, 180� and 0� for D1, D2 and D3,respectively.

All the investigated dihedral angles i.e. D1, D2 and D3are listed in Table 5. From the data it is clear that noneof them have the perfect angle (180� or 0�, whereverrequired) to give structural planarity. Therefore none ofthe eight dipeptides studied have a planar amide plane.All other dihedrals exhibit deviations from their expectedvalues with the large difference seen in ‘D’. Deviation ofdihedral angle �161� (Table 6, deviation from 180�) isreported, pointing towards the fact that the geometryaround the amide plane nitrogen i.e. 22N is not planar.

-200 -150 -100 -50 0 50 100 150 200-1456805

-1456800

-1456795

-1456790

-1456785

-1456780

-1456775

-1456770

-1456765

-1456760

Cal

cula

ted

ene

rgy

/ kJ

mol

-1

Dihedral angle / Degree

C

D

A

B

Fig. 3. Plot of dihedral angle vs. calculated energy for the –CH2Ph grouprotation in phenylalanine.

Table 6Deviation (calculated) from 180� in ‘D’ and the corresponding value for ufor the peptide bond [7C–22N] in the eight dipeptides studied

A-amino acid –R group ‘D’ (deviation from 180�) u (�)

Asn –CH2(CONH2) �7.9 �141.90Asp –CH2(COOH) �21.51 �118.90Ser –CH2OH �10.85 �152.02Cysa –CH2SH �161.29 �159.93Gly –H �7.89 15.43Tyr –CH2Ph(OH) �17.48 �113.96Val –CH(CH3)2 �8.34 �156.40Phe –CH2Ph �11.29 �157.23

a For Cys: C(24) will be C(23).


Along with the calculated deviation from 180� in ‘D’ Table6 presents the value of u for the peptide bond [22N–24C]joining phenylalanine with each of the A-amino acids.Table 6 also illustrates the trend of the values of u withthe change of –R group of A-amino acid residues. Similarstudy had been done by our group [36] and Keefe et. al. [41]where different amino acid was (fixed) at N-terminus posi-tion and varied the C-terminus position with eight otheramino acids. After a thorough study with different Phe-Acombination we conclude the hydrogen bonding (H- bond-ing) between amide plane hydrogen 19H and oxygen 27O ofcarboxylic acid terminus of dipeptide plays the major rolefor determining the values of ‘D’. Cystine (at C-terminusposition) of Phe–Cys combination shows stronger deviationof ‘D’ (Table 6). In this case, the distances between 30O and34H along with 11O and 2H are �2.2 A and 2.5 A, respec-tively, clearly indicating towards good H-bonding andhence a stronger deviation of ‘D’ (�161.29�) is observed.The dipeptides studied in this paper do not show any gen-eral trend in the deviation of ‘D’ values from 180�. We feelthe observed change in the ‘D’ as well as u values can becumulative effect of the steric hindrance (R group ofA-amino acid residue) and possible H-bonding. The inter-atomic distances (between O and H) are compatible to weakhydrogen bonding in peptide systems [42].

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-1456800

-1456795

-1456790

-1456785

-1456780

-1456775

-1456770

-1456765

Cal

cula

ted

en

erg

y / k

J m

ol-1


F

G

H

Fig. 4. Plot of dihedral angle vs. calculated energy for the –COOH grouprotation in phenylalanine.

3.4. Potential energy scan (PES) for phenylalanine:

Barriers to rotation

The potential energy scan is performed on phelylalanine.Three separate rigid potential energy surface scan has beendone: (a) by rotating the –R group of phelylalanine i.e.–CH2Ph group (b) by rotating the carboxyl group i.e.–COOH group and (c) by rotating the –NH2 group ofthe same amino acid. From the rotation of different groupsthe minimum energy conformation is obtained and valu-able structural information about protein can be obtained.

At first the geometry of phenylalanine was optimized atDFT-B3LYP level with 6-31G* basis set. The kmax valuefor phenylalanine with water as solvent is calculated byDFT method applying B3LYP correlation with 6-31G*basis set on the energy optimized geometry. The calculatedkmax value for phenylalanine (kmax � 266 nm) is well in

agreement with the experimental value (kmax � 260 nm)[43]. This suggests that the choice of method along withthe basis set has been done precisely for phenylalanine.The same method and basis (DFT-B3LYP/6-31G*) isapplied for all PES calculation of phenylalanine. A rigidpotential energy surface scan was performed on the opti-mized geometry of phenylalanine with the same method(DFT-B3LYP/6-31G*) by rotating the-R group between�180� and +180� with the increment of 10� [dihedral angleof atom 9C and 1N with respect to the bond 5C–3C,Fig. 3]. Here, the –R group is rotated between �180� and+180� with an interval of 10� keeping the rest of the phelyl-

alanine molecule fixed. Similarly another rigid potentialenergy surface scan was performed for carboxyl groupwithin the range of �180� to +180� with 10� interval [dihe-dral angle of atoms 22O and 5C with respect to bond 3C–5C]. Here, the carboxyl group is rotated likewise keeping

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-1456790

-1456785

-1456780

-1456775

Cal

cula

ted

en

erg

y / k

J m

ol -1


I

J

K

Fig. 5. Plot of dihedral angle vs. calculated energy for the –NH2 grouprotation in phenylalanine.


the rest part rigid. As mentioned earlier, similar kind ofrigid potential energy scan was performed for –NH2 groupwithin the range of +180� to �180� with an interval of 10�[dihedral angle of atoms 2H and 5C with respect to bond1N–3C]. The energy curves for all the –CH2Ph, –COOHand –NH2 group rotation of phelylalanine are given inFig. 3, Fig. 4 and Fig. 5, respectively.

The energy curve for –CH2Ph group (i.e. –R group) rota-tion of phenylalanine is given in Fig. 3. From the curve it is

Fig. 6. Highest and lowest energy conformations of phenylalanine when –CH2PB, lower energy conformation (�60�); C, highest energy conformation (�120�);Fig. 3.

observed that two maxima are there (‘C’ and ‘D’), of which‘D’ is of lower energy (ED = �1456777 kJ mol�1) and ‘C’is of higher energy (EC = �1456763 kJ mol�1). The confor-mation of phenylalanine for the maximal position (‘C’ and‘D’) is the eclipsed conformations. In the highest energy max-ima (‘C’), the most bulkier –CH2Ph group and the –COOHgroup are eclipsed to each other in phenylalanine, whereas incase of ‘D’ the –NH2 group and the –CH2Ph groups areeclipsed to each other. Due to this ‘D’ reside at lower energymaxima. Two energy wells are also identified in the curve(Fig. 3) signifying two staggered conformations ‘A’and ‘B’, respectively (EA = �1456801 kJ mol�1 andEB = �1456791 kJ mol�1). In the lowest energy conformer(‘A’) the –COOH group and the –CH2Ph group are perfectlystaggered. Whereas in the other conformation (‘B’) the–COOH and –CH2Ph groups are not perfectly staggered,due to this the energy of ‘B’ is a bit higher .The barrier of rota-tion �24 kJ mol�1. This large energy barrier indicate thatthe rotation of a bulky –CH2Ph group is very muchrestricted and the idea can be extended to predict that theenergy barrier will be higher with the increasing size of the–R group. Structure of highest and lowest energy conformersare given in Fig. 6.

The potential energy curve for the rotation of –COOHgroup of phenylalanine is given in Fig. 4. The highest andlowest energy conformers are significant to the rotationof 22O and 5C with respect to bond 6C–3C. The maximalposition of the curve i.e. the highest energy conformer (‘H’)(EH = �1456769 kJ mol�1) has its dihedral angle �10�.

h group is Rotated: A, minimum energy conformation of the plot (��60�);and D, higher energy conformation (�0�). All the conformations related to

Fig. 7. F, Lowest energy conformer (��80�); G, lower energy confor-mation (�80�); and H, highest energy conformer (�10�). All theconformations related to Fig. 4.

Fig. 8. K, Highest energy conformer (�10�); I, lowest energy conformer(��70�); and J, lower energy conformer (�160�). All the conformationsrelated to Fig. 5.


Two low energy conformers (‘F’ and ‘G’) are identified(EF = �1456801 and EG = �1456791 kJ mol�1). The–COOH group and –CH2Ph groups are perfectly staggeredand the presence of hydrogen bonding between 10O and2H (hydrogen bond distance = 2.3 A) gives the extra stabil-ity by lowering energy of the lowest energy conformer (‘F’).The energy gap between the two low energy conformers(‘F’ and ‘G’) is 10 kJ mol�1. The barriers of rotation are�32 and �22 kJ mol�1 for ‘F’ and ‘G’, respectively. Thestructure of highest and low energy conformers duringthe rotation of –COOH group of phenylalanine is given inFig. 7.

Fig. 5 shows the energy curve for the rotation of –NH2group in phenylalanine with all the other parts remainingrigid. The highest energy conformer of the energy curve is‘K’ (EK = �1456775 kJ mol�1). In the lowest energy con-former (‘I’, EI = �1456801 kJ mol�1), the –CH2Ph and–NH2 groups are not fully eclipsed and a hydrogen bondinginteraction is present between 10O and 2H (hydrogen bonddistance = 2.4 A). The other low energy conformer is ‘J’(EJ = �1456793 kJ mol�1). For this there is no evidenceof hydrogen bonding. Two barriers of rotation are of �26and �18 kJ mol�1 for conformation ‘I’ and ‘J’, respec-

tively. The highest and low energy conformers during therotation of –NH2 group of phenylalanine is given in Fig. 8.

4. Conclusion

The different structural parameters studied in this articlesupply valuable information about the structural propertyand conformational stability of small amino acid sequencesand ultimately the protein structure. Geometry optimiza-tions by applying DFT-B3LYP/6-31G* level of theory givesmuch refined energy values than that obtained by HF/6-31G* method. From bond angle, bond length data obtainedafter rigorous calculations do not vary much which ulti-mately suggests that the amide plane is almost fixed. Thepotential energy scan on phenylalanine molecule was doneby DFT method applying B3LYP correlation with 6-31G*basis set. The theoretical calculations of the kmax value ofphenylalanine with the same method and basis i.e. DFT-B3LYP/6-31G* shows nice agreement with the experimentalvalue of kmax suggesting that the choice of the method andbasis for PES calculation on phenylalanine is precise. Thepotential energy scans for phenylalanine by rotating –CH2Ph(i.e. –R), –COOH and –NH2 groups shows energy barrier of


24, 32 and 26 kJ mol�1, respectively indicate that thestructure is rigid. Big energy barrier in phenylalanine suggeststhe rigidity in a protein’s structure. This rigidity will be pres-ent not only in the backbone but also in the orientation of the–R group, as in the case of –CH2Ph group rotation in phen-

ylalanine. A consideration which should be mentioned at thispoint is the methodology used for performing the study.During the rotation of the groups (i.e. –CH2Ph, –COOHand –NH2), all other parameters remained fixed. Conforma-tional changes in the other atoms, however, may exits as thegroups rotate. This could possibly lower the barrier of rota-tion. As the large barrier is considered for all three rotations,it is assumed that any lowering in energy from conforma-tional changes would be negligible.

Acknowledgement

The financial support of DST and UGC, New Delhi isgratefully acknowledged for this work.

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