Studies of solvent effects on conformers of glycine molecule

Journal of Molecular Structure (Theochem) 617 (2002) 99–106 www.elsevier.com/locate/theochem

Studies of solvent effects on conformers of glycine molecule P. Selvarengan, P. Kolandaivel* Department of Physics, Bharathiar University, Coimbatore 641 046, India Received 8 April 2002; accepted 27 June 2002

Abstract Conformational stability and solvent effects on selected conformers of glycine under different environment, such as polar and apolar solvents have been studied using ab initio and density functional theory (DFT) methods. The molecular geometries have been optimized using HF/6-31 þ Gp method of ab initio and B3LYP/6-31 þ Gp and B3PW91/6-31 þ Gp hybrid DFT methods. The effects of solvent on the geometrical parameters, relative stability and physical properties, such as dipole moment, etc. have been studied for the conformers of glycine. q 2002 Elsevier Science B.V. All rights reserved. Keywords: Ab initio; Density functional theory; Maximum hardness principle; Polar and apolar solvents

1. Introduction A problem of considerable interest for the understanding of the chemistry of peptides and proteins is the determination of the most stable configurations of the macromolecules in solution. There is, of course a complementary but related problem of the structural organization of the solvent around the macromolecules. Nowadays, continuum models have become one of the most popular methods of incorporating solvent effects on chemical systems [1 – 3]. The solvent interaction with the solute has a considerable impact on the structural properties of the solute. Although gas phase quantum chemical calculations can frequently reproduce the essential features of chemical processes, there is a great variety of examples where the interaction with the surroundings must be explicitly included in order to obtain not only quantitative but also qualitative agreement with * Corresponding author. Fax: þ 91-422-422387. E-mail address: [email protected] (P. Kolandaivel).

experiments [4]. Amino acid chemistry in solution is one of these examples. This provides information on pair wise solute – solvent interactions. Detailed knowledge of the conformational behavior and the interaction of amino acids with solution are important to understand hydration of proteins. It is well known that glycine molecule, the smallest amino acid, found in its neutral form is stable in gas phase, whereas the zwitterionic form dominates in aqueous media [5]. Many theoretical and experimental works have been done on the conformational stability of glycine in gas phase and also zwitterionic nature of glycine in aqueous solution. A few investigations on conformational stability of neutral glycine in aqueous solution have been performed, because it possesses the zwitterionic nature in liquid phase. There has been no much attention paid to study the order of stability of conformers of glycine in polar and apolar solvents. The conformational flexibility of glycine in liquid phase shows the second most stable conformer in gas phase as the most stable one, because of its large dipole moment. So the second

0166-1280/02/$ - see front matter q 2002 Elsevier Science B.V. All rights reserved. PII: S 0 1 6 6 - 1 2 8 0 ( 0 2 ) 0 0 4 2 1 - 9

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most stable conformer of glycine easily forms the zwitterion. In the present investigation, six most stable conformers of glycine (Ip, IIn, IIIn, IVn, Vn, VIp, where p refers to heavy atoms in planar arrangement and n refers to non-planar arrangement) have been taken to study the relative stability of the conformers of glycine in both apolar (cyclohexane, acetone) and polar solvent (water). An attempt has been made to study the validity of maximum hardness principle (MHP) through chemical hardness and chemical potential for glycine conformers in the different environments, and also the effect of electrostatic attraction and solvent interaction on the atomic charges of conformers of glycine have been studied.

2. Computational details The different conformers of glycine have been optimized by using ab initio and density functional theory (DFT) methods. In DFT method, Becke’s three parameter exact exchange functional (B3) [6] combined with the gradient corrected functional of Lee –Yang– Parr (LYP) [7] and Predew and Wang’s 1991 (PW91) [8] were used by implementing the 6-31 þ Gp basis set. It is well known that the basis set should include one set of diffuse function for studying the inter- and intra-molecular interactions. The same basis set is used for HF-SCF level of theory also. The chemical hardness h and chemical potential m have been calculated using the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies determined from MP2/ 6-31 þ Gp level of theory. The net atomic charges of glycine molecule are also computed at B3LYP/ 6-31 þ Gp level of theory. The solvent effects were investigated by using Tomasi and co-workers [9] selfconsistent isodensity polarizable continuum model (SCI-PCM) of self-consistent reaction field (SCRF) calculations. All computations have been performed on GAUSSIAN 98W package [10].

3. Results and discussion The optimized geometrical arrangements and labeling of atoms of the conformers of glycine are shown in Fig. 1. The geometrical parameters

Fig. 1. Conformers of glycine considered in this study and their numbering.

calculated by HF/6-31 þ Gp level of theory are ˚ and , 1.58 for bond length slightly deviated (, 0.01 A and bond angle, respectively) from the values of DFT methods. The structural parameters calculated by DFT methods, B3LYP/6-31 þ Gp and B3PW91/631 þ Gp are found to be similar and are comparable with the available experimental and high cost second order Møller –Plesset (MP2) gas phase results [11]. Hence, it is enough to discuss about the structural parameters of the different conformers calculated at B3LYP/6-31 þ Gp level of theory at different media. The geometrical parameters of glycine conformers are strongly affected by the influence of the solvents and are summarized in Table 1. The tabulated values indicate that the bond lengths C1 – H3 and N5 – H9 are approximately same at all the medium. The reason is that, the interaction of hydrogen atom on the medium is less, but the side chains are strongly affected by the solvent particularly, interaction with water molecule. The calculated C1 –C2 bond length is not changed, from gas phase to aqueous media through cyclohexane and acetone for all the conformers except the conformers II and VI. The C1 – C2 bond length of ˚ at gas conformer II is 1.540, 1.537, 1.534, and 1.534 A phase, cyclohexane, acetone and water medium, respectively, and in conformer VI the bond length

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Table 1 Structural parameters of studied conformers of neutral glycine computed at B3LYP/6-31 þ Gp level of theory Parameters

Gas phase ð1 ¼ 1:0Þ

Cyclohexane ð1 ¼ 2:0Þ

Acetone ð1 ¼ 20:7Þ

Water ð1 ¼ 78:5Þ

Calc.

Expt.a

Conformer 1 R(C1– C2) R(C1– H3) R(C1– N5) R(C2– O6) R(C2yO7) R(O6–H8) R(N5–H9) u(N5C1C2) u(O6C2C1) u(O7C2C1)

1.527 1.097 1.450 1.357 1.213 0.976 1.018 115.8 115.5 125.7

1.529 1.093 1.466 1.340 1.204 0.966 1.001 113.0 111.5 125.0

1.526 1.097 1.451 1.354 1.214 0.977 1.018 115.9 111.5 125.6

1.525 1.097 1.452 1.35 1.217 0.977 1.018 116.0 111.6 125.3

1.525 1.097 1.452 1.349 1.218 0.977 1.018 111.7 111.7 125.3

Conformer 2 R(C1– C2) R(C1– H3) R(C1– N5) R(C2– O6) R(C2yO7) R(O6–H8) R(N5–H9) u(N5C1C2) u(O6C2C1) u(O7C2C1)

1.540 1.095 1.472 1.342 1.210 0.991 1.016 111.3 114.1 122.5

1.532 1.094 1.465 1.341 1.207 0.980 1.012 111.0 113.8 112.6

1.537 1.095 1.470 1.340 1.213 0.995 1.016 110.9 113.9 123.0

1.534 1.095 1.468 1.337 1.218 1.003 1.016 110.3 113.7 123.6

1.534 1.095 1.468 1.337 1.218 1.003 1.016 110.1 113.7 123.7

Conformer 3 R(C1– C2) R(C1– H3) R(C1– N5) R(C2– O6) R(C2yO7) R(O6–H8) R(N5–H9) u(N5C1C2) u(O6C2C1) u(O7C2C1)

1.529 1.097 1.452 1.357 1.213 0.977 1.017 119.3 113.4 124.1

1.519 1.095 1.452 1.357 1.210 0.968 1.014 117.9 112.1 124.9

1.528 1.096 1.454 1.347 1.219 0.977 1.018 119.1 113.7 123.5

1.528 1.096 1.454 1.346 1.220 0.977 1.018 119.1 113.7 123.8

1.528 1.096 1.454 1.346 1.220 0.977 1.018 119.1 113.7 123.8

Conformer 4 R(C1– C2) R(C1– H3) R(C1– N5) R(C2– O6) R(C2yO7) R(O6–H8) R(N5–H9) u(N5C1C2) u(O6C2C1) u(O7C2C1)

1.514 1.107 1.456 1.355 1.212 0.976 1.018 110.2 111.8 125.2

1.508 1.102 1.454 1.353 1.213 0.968 1.014 111.1 110.1 125.0

1.514 1.106 1.458 1.353 1.214 0.977 1.018 110.5 111.8 125.2

1.514 1.105 1.459 1.349 1.217 0.977 1.019 111.2 111.6 125.3

1.514 1.105 1.460 1.349 1.217 0.977 1.019 111.2 111.5 125.3

Conformer 5 R(C1– C2) R(C1– H3)

1.516 1.107

1.510 1.102

1.516 1.106

1.516 1.105

1.516 1.105 (continued on next page)

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Table 1 (continued) Parameters

Gas phase ð1 ¼ 1:0Þ

Cyclohexane ð1 ¼ 2:0Þ

Acetone ð1 ¼ 20:7Þ

Water ð1 ¼ 78:5Þ

a

Calc.

Expt.

R(C1 –N5) R(C2 –O6) R(C2yO7) R(O6–H8) R(N5–H9) u(N5C1C2) u(O6C2C1) u(O7C2C1)

1.462 1.357 1.212 0.976 1.017 112.5 112.1 125.1

1.460 1.356 1.208 0.968 1.014 111.1 110.9 125.8

1.462 1.353 1.215 0.976 1.018 113.0 112.5 124.7

1.463 1.346 1.219 0.977 1.018 113.6 113.2 123.9

1.463 1.346 1.219 0.977 1.018 113.6 113.2 123.8

Conformer 6 R(C1 –C2) R(C1 –H3) R(C1 –N5) R(C2 –O6) R(C2yO7) R(O6–H8) R(N5–H9) u(N5C1C2) u(O6C2C1) u(O7C2C1)

1.537 1.099 1.448 1.364 1.205 0.973 1.018 115.9 115.5 124.4

1.529 1.096 1.445 1.356 1.203 0.964 1.014 115.6 115.1 124.4

1.536 1.099 1.449 1.360 1.209 0.973 1.018 115.9 115.7 124.4

1.534 1.098 1.451 1.353 1.214 0.974 1.018 116.0 116.1 124.3

1.534 1.098 1.451 1.353 1.214 0.974 1.018 116.0 116.2 124.3

a

Experimental values taken from Ref. [11].

˚ . This is due to the varies from 1.537 to 1.534 A increase in solvent interaction as the polarity of the medium increases. Similarly, the C1 – N5 bond strength decreases in all the conformers except conformer II as the dielectric constant of the medium increases. In conformer II, the bond length is 1.472, ˚ , respectively. The C2 – O6 bond 1.470, 1.468, 1.468 A length decreases from gas phase to polar media. This is because the oxygen atom is more electronegative and has lone pair electrons that are easily interacting with the solvents. It is observed that both ab initio and DFT methods predict approximately the same bond angles u(C1C2O6), u(N5C1C2) for all the conformers from gas phase to aqueous media. Indeed, based on quantum chemical calculations Ra¨sa¨nen et al. [12] proposed a rule known as trans-angle rule which states, “if in a conformer of primary alcohol or amine a CC or CH bond is trans to an XH bond (X ¼ O, N), the corresponding XCC or XCH angle will be considerably smaller than that for other configurations.” The validity of this rule for glycine conformers in gas phase has already been verified [11]. This rule is also valid for the conformers of

glycine in apolar and polar solvents. In all the environments, the bond angle u(N5C1C2) varies from 109.8 to 119.38 and u(C1C2O6) from 111.7 to 116.38. This large variation is due to intra-molecular hydrogen bonding and with the electrostatic interaction of the solvent. In the present investigation, we conclude that the solvent interactions mainly take place only at the atoms having lone pair electrons and it is less for other atoms. The dipole moments of various conformers of glycine computed at B3LYP/6-31 þ Gp level of theory in different environments are shown in Table 2. The calculated dipole moments in gas phase are comparable with the available experimental results [11]. For all the conformers dipole moment increases as the dielectric constant of the medium increases. It is noted that the order of solubility of each conformer decreases in the order water . acetone . cyclohexane . gas phase. In the present study, the conformer II has higher value of dipole moment in all media, the reason for larger dipole moment is due to the stronger hydrogen bonding interaction compared with other conformers that tends to high electrostatic interaction and large

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Table 2 Total energy E (in hartree), relative energy DE (in kcal/mol), dipole moment mM (in Debye), chemical hardness h (in eV), and chemical potential m (in eV) of studied conformers of glycine Parameters

Gas phase B3LYPa

Cyclohexane B3PW91

B3LYP

– – ,1.00

0.44609 0.0 1.411 6.58 24.55

0.33636 0.0 1.449

0.45233 0.0 1.728 6.64 24.35

0.34281 0.0 1.771

0.44729 20.75 6.525 6.59 24.85

0.33832 21.23 6.597

0.45603 22.32 7.344 6.67 24.57

0.34732 22.83 7.440

0.45694 22.47 7.429 6.68 24.54

0.34826 22.98 7.530

0.44403 1.29 2.208 6.45 24.46

0.33433 1.27 2.24

0.45065 1.05 2.638 6.52 24.24

0.34118 1.02 2.678

0.45137 1.02 2.690 6.52 24.22

0.34192 0.99 2.730

0.44346 1.65 2.478 6.47 24.45

0.33357 1.75 2.480

0.45009 1.41 3.012 6.55 24.30

0.34045 1.48 3.030

0.45083 1.36 3.073 6.55 24.28

0.34123 1.43 3.092

0.44191 2.62 2.771 6.49 24.48

0.33193 2.78 2.737

0.44869 2.28 3.045 6.54 24.28

0.33902 2.38 2.969

0.44944 2.23 3.082 6.54 24.27

0.33981 2.32 2.958

0.43682 4.69 3.512 6.59 24.60

0.32896 4.64 3.507

0.44810 2.65 4.131 6.64 24.35

0.33868 2.59 4.135

0.44918 2.40 4.207 6.64 24.31

0.33980 2.33 4.217

E(2284) DE mM hc m

0.44195 0.0 1.232 6.53 24.73

0.33209 0.0 1.261

II

E(2284) DE mM h m

0.44123 0.45 5.976 6.50 25.05

0.33211 20.01 5.964

–

E(2284) DE mM h m

0.43965 1.44 1.967 6.40 24.66

0.32981 1.43 1.990

–

E(2284) DE mM h m

0.43928 1.68 2.195 6.42 24.61

0.32925 1.78 2.191

–

E(2284) DE mM h m

0.43753 2.77 2.580 6.46 24.66

0.32737 2.96 2.549

–

E(2284) DE mM h m

0.43270 5.81 3.154 6.52 24.85

0.32291 5.76 3.146

–

IV

V

VI

a b c

Water

Exptb

I

III

Acetone

1.78625 5.59

1.78479 1.90

1.78507 2.06

0.78358 2.41

1.77799 2.95

B3PW91

B3LYP

B3PW91

B3LYP 0.453 0.0 1.766 6.64 24.34

B3PW91 0.34351 0.0 1.814

6-31 þ Gp basis set have been used for DFT methods. Experimental values taken from Ref. [11]. Chemical hardness and chemical potential computed at MP2/6-31 þ Gp.

polarization when the solute interacts with solvent. As mentioned in theoretical and experimental results [13], the present study also confirmed the second most stable conformer in gas phase is the most stable one in liquid phase. Because of the high polarity, it easily passes to zwitterionic nature. The dipole moment of conformer II at B3LYP/6-31 þ Gp level of theory is 7.429 and 5.976 D, respectively, in aqueous solution and gas phase. The sixth stable

conformer in the gas phase is having second high polarity in liquid phase, and its dipole moment is 3.154 and 4.207 D in gas phase and aqueous solution, respectively. The conformer V has third large solubility, the dipole moment increases from gas phase to polar media as 2.580 and 3.082 D, respectively. The most stable conformer in gas phase has the least polarity in aqueous solution. The calculated dipole moment versus dielectric

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II . I . III . IV . V . VI. The change in the stability of the conformer in liquid phase is between conformer II and I only; all other conformers remain same as in gas phase. In the present study, we conclude that, when neutral glycine conformer undergoes polar and apolar solvents the order of stability is not affected. The chemical hardness and chemical potential are the two important quantities, which help to characterize the chemical system: these are defined as

h¼

Fig. 2. Variation of the dipole moment of the glycine conformers for different solvents.

constant of the various solvents is shown in Fig. 2. The solubility of the conformers is in the order of II . VI . V . IV . III . I. The present study indicates that possibility of forming the zwitterions in the liquid phase is same of the above order. As has been determined both experimentally and theoretically the lowest energy form of neutral glycine in the gas phase is Ip. In the present study, the second most stable conformer in gas phase is the most stable conformer in liquid phase. The variation of relative energy with conformers are shown in Fig. 3. The relative energies of the conformers decrease from gas phase to aqueous phase through apolar solvents and also the stability of the conformer increases. The relative energy of the second conformer in gas phase to liquid phase is 0.45, 2 0.75, 2 2.32, and 2 2.47 kcal/mol, respectively. The order of stability of the neutral glycine conformer in the liquid phase is

Fig. 3. Variation of relative energy with conformers.

I2A ; 2

m¼2

IþA 2

where I ¼ 2EHOMO and A ¼ 2ELUMO ; I and A are the ionization potential and electron affinity of the molecules. We have calculated h and m for glycine conformers using the above equations in single point energy calculations at MP2/6-31 þ Gp level of theory and are presented in Table 2. From the results, it is noted that the hardness and chemical potential of each conformer increases from gas phase to liquid phase. The values are increased in the following order: water . acetone . cyclohexane . gas phase. This order agrees well with the order of stability arrived from the relative energies. This shows that the glycine conformers have higher stability in the liquid phase than the gas phase. In gas phase, conformer I has the maximum hardness (6.53 eV) and in liquid phase conformer II has the maximum hardness (6.59 eV, 6.67 eV in apolar and 6.68 eV in polar media), respectively. The conformer II has the largest deviation of hardness value, i.e. 0.18 eV from gas to liquid phase when compared to other conformers. The reason behind this is, glycine conformer having hydrogen bond interaction between amine group and carboxyl group contribute maximum energy to stabilize the molecule. During the formation of hydrogen bond, the charge transfer may change the potentials vðrÞ and m, which are playing major role for the MHP. By considering the calculated hardness the order of stability of the conformers in gas phase is I . VI . II . V . IV . III. The order of stability in cyclohexane is II . VI . I . V . IV . III. The order in acetone and in water is the same as II . I . VI . IV . V . III. As from earlier studies on nitrosoethylene [14], it is seen that MHP could not predict the stability of the system having hydrogen bonding interactions. Similar type of trend is observed

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atom is bonded with two hydrogen atoms; it gains more charges from H3 and H4 atoms and C2 atom is bonded with two oxygen atoms which has lone pair electrons. These two oxygen atoms gain more charges from C2 atom leaving C2 as more positive. As the polarity of the medium increases, the atomic charges of the atoms in all the conformer increase except C1 atom in conformer II, which is due to large dipole moment in this conformer. When the dielectric constant of the medium increases, there is an increase in dipole moment and also large charge transfer between amine group and carboxyl group that cause decrease of C1 atomic charges in conformer II. In all the media, the charge of C1 atom in conformer III is less negative (2 0.256 to 2 0.265) and that of C2 is less positive (0.397 to 0.453) than all the other conformers. The reason behind this is that there is no hydrogen bond interaction in conformer III that causes less charge transfer between the atoms. Two

in our present investigation and hence we conclude that MHP could not predict the order of stability of the conformers of glycine in a particular medium but it can predict the order of stability in different media. The net atomic charge can provide a simple and intuitive way to rationalize the chemical reactivity. It can be evaluated by means of appropriate partitioning of the charge distribution. One widely used method for partitioning is Mulliken Population Analysis (MPA) [15]. The net atomic charges of glycine can provide the evidence of charge transfer and polarization between two hydrogen bonded fragments. Table 3 shows the atomic charges of atoms of various conformers of neutral glycine in different environment computed at B3LYP/6-31 þ Gp level of theory. In general, the atomic charges of individual atoms are strongly affected by the interaction of atoms with solvents. In our present investigation, C1 has negative charge and C2 has positive charge. This is because C1

Table 3 Atomic charges of various conformers of glycine in different environment computed at B3LYP/6-31 þ Gp Medium

Conformers

C1

C2

H3

H4

N5

O6

O7

H8

H9

H10

Gas phase

1 2 3 4 5 6

20.374 20.378 20.256 20.41 20.393 20.436

0.512 0.560 0.397 0.585 0.580 0.563

0.232 0.234 0.236 0.209 0.206 0.224

0.232 0.234 0.236 0.227 0.229 0.224

20.836 20.918 20.858 20.79 20.798 20.836

20.577 20.564 20.58 20.575 20.614 20.571

20.458 20.465 20.459 20.485 20.469 20.433

0.481 0.512 0.494 0.481 0.491 0.468

0.394 0.393 0.395 0.388 0.387 0.339

0.394 0.393 0.395 0.37 0.380 0.339

Cyclohexane

1 2 3 4 5 6

20.376 20.373 20.259 20.422 20.394 20.425

0.529 0.567 0.414 0.609 0.59 0.565

0.236 0.240 0.239 0.216 0.214 0.233

0.236 0.242 0.239 0.23 0.232 0.233

20.857 20.934 20.878 20.808 20.817 20.857

20.593 20.574 20.592 20.591 20.626 20.588

20.48 20.499 20.484 20.507 20.493 20.462

0.501 0.518 0.514 0.501 0.511 0.492

0.401 0.409 0.403 0.39 0.392 0.405

0.401 0.405 0.403 0.38 0.391 0.405

Acetone

1 2 3 4 5 6

20.377 20.366 20.265 20.450 20.401 20.402

0.561 0.579 0.449 0.656 0.612 0.568

0.241 0.250 0.241 0.227 0.234 0.244

0.241 0.250 0.241 0.235 0.236 0.244

20.890 20.960 20.909 20.837 20.848 20.890

20.625 20.589 20.619 20.625 20.652 20.628

20.515 20.547 20.523 20.540 20.531 20.509

0.541 0.526 0.553 0.541 0.551 0.543

0.412 0.429 0.416 0.392 0.399 0.415

0.412 0.429 0.416 0.402 0.409 0.415

Water

1 2 3 4 5 6

20.377 20.366 20.265 20.453 20.401 20.399

0.565 0.581 0.453 0.661 0.615 0.569

0.241 0.251 0.241 0.228 0.227 0.245

0.241 0.251 0.241 0.235 0.235 0.245

20.894 20.963 20.913 20.841 20.852 20.893

20.629 20.591 20.622 20.629 20.656 20.634

20.519 20.553 20.527 20.544 20.535 20.514

0.546 0.526 0.558 0.546 0.556 0.551

0.413 0.431 0.417 0.393 0.400 0.415

0.413 0.432 0.417 0.404 0.411 0.415

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lone pair electrons of nitrogen atom attract more charges from the neighboring hydrogen atoms, so the nitrogen atom has more negative charges than the other atoms.

4. Conclusions The ab initio and DFT studies have been performed on neutral glycine molecule to study the order of stability and solubility of the molecule in apolar and polar solvents. The order of the solubility of the conformers of the title molecule in polar and apolar media is II . VI . V . IV . III . I. So glycine acquires zwitterionic nature in the above order. The order of stability of the molecule in polar and apolar media is II . I . III . IV . V . VI. From that we conclude, in liquid phase, stability of the system not only depends on the large dipole moment but also depends on the presence of hydrogen bonding interaction and interaction with the solvents. MHP could predict the stability of the molecule in different media, but it could not predict the order of stability in each media because of the presence of hydrogen bonding interaction.

Acknowledgments The authors are thankful to DST, Government of India, for the financial support for this work in the form of project.

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