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L-asparagine crystals with wide gap semiconductor features: Optical absorption

measurements and density functional theory computations
G. Zanatta, C. Gottfried, A. M. Silva, E. W. S. Caetano, F. A. M. Sales, and V. N. Freire

Citation: The Journal of Chemical Physics 140, 124511 (2014); doi: 10.1063/1.4869179
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By varying the lattice parameters from their converged equilibrium values. it would be very Asparagine (Asn.17. Reuse of AIP content is subject to the terms at: http://scitation. on the other hand. NH2 · · ·CO(NH2 ).32 eV. A. W.7 Besides.022 Å. predict a main band gap of 5. 60455-760 Fortaleza-CE. deamidation accelerates amyloid formation3 ).5 the effect of solvent molecules. Three other indirect band gaps of 4.1 A. 90035-003 Porto Alegre-RS. with chemical formula C4 H8 N2 O3 . The optical absorption measurements revealed that the anhydrous monoclinic L-asparagine crystal is a wide band gap material with 4.1063/1. Freire4 1 Departamento de Bioquímica. Caetano.95 eV main gap energy. Finally. aqueous media. Asn deamidation is a key aspect dle of Fig. Thus. with the global energy minimum being stabilized sity functional theory (DFT) framework.2 E. 64260-000 Piripiri-Pi. The lattice parameter differences a. process that affects biological functions. a theoretical/experimental matrix- related to the stability of protein pharmaceuticals4 and pro- isolation FT-IR study of the conformational behavior and H- teomic sample preparation.8 The Asn deamidation reaction bond structure of asparagine was undertaken by Boeckx and path and its multitude of subproducts is related to the ring Maes. as shown at the top and mid- paragine sites.179 On: Wed. Universidade Federal do Ceará. Brazil (Received 14 November 2013. respectively. glycoproteins and. It has an essential role on the biosynthesis of solid state. c between theory and experiment were as small as 0. Brazil 3 Instituto de Educação. pH-dependent mechanism. b. N. Sales. forming a network and their role in nonenzymatic peptide bond cleavage at as- of intramolecular interactions. but the mass values allow for some charge mobility except along a direction perpendicular to the molecular layers of L-asparagine which form the crystal. 29 Oct 2014 01:59:10 .36 eV are assigned to α3 → . and 0. been performed by Chen et al. Grimme) was employed to perform the calculations. tamers. just 50 meV above the experimental value. INTRODUCTION formation tendency of the asparagine molecular structure (see top right side and middle of 0. so anhydrous monoclinic L-asparagine crystals could behave as wide gap semiconductors.6 C=O· · ·NH2 . Silva.4869179] I. after further optimization. Recently.4 and V. and (CO)NH2 · · ·CO(OH). THE JOURNAL OF CHEMICAL PHYSICS 140. N). on the other the most stable containing only 3 intramolecular H-bonds: 0021-9606/2014/140(12)/124511/14/$30. Density functional theory (DFT) within the generalized gradient approximation (GGA) including dispersion effects (TS. C 2p–side chain. we show that the unit cell is less stiff along the b direction than for the a and c directions. Universidade Federal do Rio Grande do Sul.020. S.aip. Gottfried.30 eV.9 for gas phase asparagine which limits the lifetime of proteins through a degradation using the B3LYP/6-311G* functional/basis set combination. with more structured curves for incident light polarized along the 100 and 101 directions. the calculations point to a high degree of optical anisotropy for the absorp- tion and complex dielectric function. a) Electronic mail: ewcaetano@gmail.1 C. [http://dx. Zanatta. under physiological conditions. Effective mass calculations suggest that hole transport behavior is more anisotropic than electron transport. published online 31 March 2014) Results of optical absorption measurements are presented together with calculated structural. 124511 (2014) L-asparagine crystals with wide gap semiconductor features: Optical absorption measurements and density functional theory computations G.3. accepted 27 February 2014. respectively. M. produced structural parameters in very good agreement with X-ray data. DFT-GGA+TS simulations. Ciência e Tecnologia do Ceará. destabi- A systematic and extensive conformational search has lizes and spontaneously deamidates into aspartic acid (Asp).00 eV. with a 4. M. The calculated band gap energy is smaller than the experimental data by about 15%. -sol computations. Brazil 2 Universidade Estadual do Piauí. they have obtained as much as 972 unique trial struc- and deteriorating therapeutic proteins. Caixa Postal 6030.23 eV indirect band gap corresponding to Z →  and Z → β transitions.10 which found ten stable low energy asparagine con- formations (total energy variation smaller than 10 kJ mol−1 ). and 4. respectively. being unveiled their by four hydrogen bonds COOH· · ·NH2 . Brazil 4 Departamento de Física. and in the ing beings. 2 leading to diseases By allowing for all combinations of internal single-bond ro- (for example.1. Downloaded to IP: 200. and α2 →  transitions. 4. a total of 62 conformers ways of Asn deamidation were investigated within the den- were found. elec- tronic. and optical properties for the anhydrous monoclinic L-asparagine crystal.4 The reaction path- tures.a) F. helpful to achieve a deeper understanding of the structural is one of the 20 amino acids which form proteins in liv- features of asparagine in vacuum. and C 2p–carboxyl orbitals contribute most significantly to the highest valence and lowest conduction energy bands. α1 → .051.41. 1. 60040-531 140. Electronic wavefunctions mainly originating from O 2p–carboxyl. © 2014 AIP Publishing LLC. 124511-1 © 2014 AIP Publishing LLC This article is copyrighted as indicated in the article. 1).

2.13 and Verbist et al. Cα –Cβ bond. intermolecular hydrogen bonds unlock asparagine as well. Raman. J. lattice effects being C=Osc · · ·HNbb .50 Å.16 respectively.30 self-assemblies terms of cage effects. biosensors and optoelectronic devices are being made. 29 Oct 2014 01:59:10 . works.12 carried out classical of D. Actually. proline on Cu(110) was studied. vacuum on Cu(110) was carried out.17 ab initio theoretical computations to predict spectroscopic pa.27 the adsorption and ordering of geometry. 124511 (2014) in aqueous solutions was discerned. 34 have proposed to This article is copyrighted as indicated in the article.9 is also shown.179 On: Wed. as the solvent polarity in- duced a break up of NH· · ·O=C bonding between the side chain and the terminal groups of asparagine.41. Chem. green back. as well as in the vacuum lowest energy conformer. the N2 H3 · · ·O2 (N1 H6 · · ·O3 ) hydrogen bond is strongly (moderately) weakened. nuclear magnetic resonance backbone) by Chen et al.. On the disregarded. Cabezas et al. Downloaded to IP: 200. and vibrational FIG. efforts to describe theoretically the role of intermolecular bonds on the properties of molecular crys- tals were made in the last few years. together with hundreds of atoms.9 as depicted in the top part of Fig. according to X-ray diffraction data of both anhydrous monoclinic P21 (Z = 2)13 and monohydrated or- thorhombic P21 21 21 (Z = 4)14–16 crystalline structures (see again the top and middle parts of Fig.11 by employing a combination of and the development of new DFT codes have allowed the ap- laser ablation (LA) with molecular beam (MB) and Fourier plication of these simulation methods to systems with up to transform microwave (FTMW) For ing that the lowest energy Asn conformer exists in the gas example. one cannot use the smallest energy isolated conformer (even in solution) to calculate the crystalline properties accurately. and Oα · · ·HNβ with hy. and the adsorption of glutamic acid on the interaction between asparagine and solvent molecules in Ag(100) was surveyed by Smerieri et al. Oda and Nakayama33. Top: Asparagine molecules in anhydrous monoclinic (A. i. gray morphs through infrared.. 19 some attempts to employ amino acid films in investigated the conformation locking of asparagine.e.31 and the hydrogen-bonded net- the solvent effect on the Asn conformational space. orange backbone) asparagine what restricted to experimental characterization of their poly- crystals.28 and Fischer conformational preference of asparagine in the gas phase and et al.18 Å. electronic. optical. L-tyrosine and L-cysteine on the Ag(111) surface was studied With the purpose of investigating the causes behind such through several techniques by Reichert et al.86 Å. The required to study such systems within the DFT formalism has hydrogen bond lengths obtained by Cabezas et al. and OHbb · · ·Nbb . 1. 1). conclud.11 are also shown for the restrained advances in the field. 1. Nβ H· · ·Oβ . a study of the adhesion of amino acids on a series phase as a result of a network of four cooperative contacts of inorganic surfaces including insulators and semiconductors Nα · · ·HO. middle: superposition of the molec. Reuse of AIP content is subject to the terms at: http://scitation. properties.aip.29 respectively. C=Obb · · ·HNsc . Research on molecular crystals has being some- bone) and monohydrated orthorhombic (M. 124511-2 Zanatta et al.18.. but without af- fecting the hydrogen bonds within the side chain and the ter- minal groups. anhydrous monoclinic and mono- hydrated orthorhombic asparagine crystals are stabilized by hydrogen bonds and van der Waals interactions which de- termine their structural. and electron paramagnetic resonance (EPR) spectro- ular configurations depicted at the top obtained through the alignment of the scopies. 1. For this reason. On the theoretical side.26 and a reactive dynamics respectively.17–24 As members of the class of molecular crystals.32 On polarization-induced conformational unlocking of asparagine the other hand.17. A solvent work of histidine on Ge(100) was examined as well. Such hydrogen bond network was also observed simulation of monolayer and multilayer adsorption of glycine by Chen et al. 140. as one can see at the bottom table of Fig.25 the adsorption footprints of drogen bond lengths of 1. (NMR). As our research group has pointed out in previous rameters for direct comparison with the experimental ones. The N2 H3 · · ·O2 and N1 H6 · · ·O3 hydrogen bond lengths increase significantly. while the N2 H2 · · ·O3 is kept by the lattice intermolecular interaction. Oβ · · ·H–Nα . Selvaraj et al..17 sake of comparison. which implies in an unlocking effect.. The DFT-calculated Asn molecular structure in vacuum (V. Even the numerous spectroscopic measurements on molecu- lar crystals are usually explained by appealing to the prop- erties of the individual molecules. as stated by Tulip and Clark. The molecular unlocking leads to Asn molecular structures in crystals that are remarkably different from those observed in vacuum and water solutions. which are very useful in the pharmaceutical domain. the increase of computational power other hand. was performed by Willett et al. However. Consequently. according to the X-ray data of Yamada et al. and 2.47 Å. bottom: intramolecular distances (in Å) for the atoms involved for example. Phys. 2.. In the solid state.and L-methionine on Au(111) surfaces were studied and Car-Parrinello molecular dynamics simulations to study by Naitabdi and Humblot. the computational cost in the formation of hydrogen bonds present in the anhydrous and monohy- drated Asn crystals.

36 as well as bionanoelectronics. 39 Hence. 2. Finally. and functions. Phys. cident radiation.23 The characterization of the band gap energy. leucine. Light properties (see Sec. anyway.179 On: Wed. 124511-3 Zanatta et al. Among the few reports already published concerning the field of amino acid crystal simulations.17. Z = 4) L- cysteine crystals. 5.20 it is also close to the 5. Opti- eV and 5. Z = 2)21 L- aspartic acid crystals. which might produce new types of biodevices. isoleucine. particularly) of amino acid crystals and films is of paramount importance for the future development of bio- optoelectronic devices. it was also with ε1/2 . previous opti- the band curves indicate that holes in anhydrous monoclinic cal absorption measurements in amino acid crystals indicate L-asparagine crystals can behave as in a semiconductor.aip.7 eV. Z = 4) α-glycine crystals. if the square root (square) of the op- pointed out that anhydrous crystals of DNA bases are wide tical absorption displays a linear behavior as a function of the gap semiconductors. electronic. As we will see later.55 eV). The curve for α 1/2 . it was suggested that anhydrous L-aspartic crystals behave as wide-gap semiconductors with higher car- The onset of the optical absorption α(ε) as a function rier mobilities for directions parallel to the L-aspartic acid of the incident photon energy ε in an indirect gap crystal molecular layers. Taking into account these curves. one can see plots for α 1/2 . exhibits an onset at about 4. a main indirect band gap is also Carrier effective masses estimated from parabolic fittings of predicted from our DFT computations. The red straight line is used to estimate the indirect band gap. while that these systems tend to exhibit indirect band gaps. in con- compatible.5 eV. which depends on their band structures. and much smaller than the 5.17.37 which could a curved onset shape beginning at about 5. while va. α. with background removal and baseline The density functional computations were carried out corrections made when necessary.38. Z = 4) L- >99% was purchased from Sigma-Aldrich. are relevant ing now to Fig.40 Lattice parameters and atomic This article is copyrighted as indicated in the article. 2. and α 2 for the for the development of bioorganic electronic and optoelec- anhydrous L-Asn–KBr pellets.19–22 A the electrons behave as in an insulator. increase up to 5. X-ray diffraction serine crystals. 29 Oct 2014 01:59:10 . One can observe that α 2 has tronic devices.23 eV value straight line tangent to the α 1/2 curve intercepts the energy assigned to Z →  and Z → β transitions between the up- axis.0 eV with a smooth linear nents. Besides. absorption measurements were carried out in these pellets us- ing a Varian Cary 5000 UV-visible NIR spectrophotometer equipped with solid sample holders.2 eV. we estimate cal absorption measurements in these crystals were also per- that the L-Asn crystal has an indirect band gap of 4. The absorption spectra III. optical absorption squared (α 2 ). bio- curve onset starts at about 4. characteristics. the un- derstanding of fundamental aspects (electronic and optical characteristics. OPTICAL ABSORPTION MEASUREMENT gap measured for anhydrous monoclinic (P21 . With these characteristics in mind and look- erties. biodegradable. monoclinic (P21 /n.95 eV was which corresponds to the energy at the point where the red obtained.19 and larger than the values for orthorhombic (P21 21 21 . low-cost. but the values of the effective masses of its crystal structure (data not presented here). root (α 1/2 ) of L-Asn-KBr pellets measured at 300 K with nonpolarized in- and glycine17–19 are wide band gap semiconductors.21–1. Optical absorption (α). some of them have FIG.41. their properties.95 eV. while the α advance the development of sustainable.21 while anhydrous L-serine crystals behave varies with ε2 .62 eV. which is close to the DFT-estimated 4. J. 124511 (2014) control electrically the amino acid ionization and the con- formation of proteins arranged on semiconductor surfaces. and square presented results suggesting that alanine. the material must have an indirect (direct) electronic of these molecular materials and their charge transport prop- main band gap. Indeed. using the CASTEP code. Reuse of AIP content is subject to the terms at: http://scitation. from which a wide indirect band gap of 4.0 eV (which we believe is an artifact of the The purpose of this work is to present the results of DFT square rooting process. V). DFT COMPUTATIONAL DETAILS of the samples were recorded in the 200–800 nm wavelength range (6. Chem. 140.22 Besides. the calculated comparison of the energy gap of anhydrous monoclinic L- optical absorption and dielectric function along some sym- asparagine crystal with the values obtained for other amino metry directions display a noticeable anisotropy for polarized acid crystals shows that it is smaller than the estimated for incident light. and mass production electronic compo- trast.0 erties of anhydrous monoclinic L-asparagine crystals. as the optical absorption in this energy calculations of the structural. line and cysteine could be small band gap isolators.02 eV II. while for a direct gap material it increases like n-type wide gap semiconductors.90 eV Anhydrous monoclinic L-asparagine powder with purity measured gap for anhydrous monoclinic (P21 21 21 . Thus. 4. 20 on the other hand. The powder was charge carriers are also necessary to know its charge transport mixed with KBr to form anhydrous L-Asn–KBr pellets.11 eV. Downloaded to IP: 200. permost valence band and the lowermost conduction band.22 The L-asparagine monoclinic crystal has a measurements were accomplished to confirm the monoclinic wide gap. and optical prop- range is very small) and a sharp linear increase between 5. Stroscio and Dutta35 described advances in man-made nanos- tructures integrated with biological molecules and systems.

in the case of the vaterite CaCO3 crystal significant differences were ob- served in the spatial pattern of the carbonate groups inside of the unit cell between experiment and DFT calculations.883 8.49 a (Å) 5.0622(4) Å. Downloaded to IP: 200.41. from which one can de- rive the infrared and Raman spectra which are dependent on the crystal geometry.929 6.13 are given in Table I. amino acid side chain type. TABLE I. Phys. N-2s2 2p3 . hydro- gen bonding pattern. 44 were carried using two dis.020 0.062 While the PBE functional leads to results close to the ones a (Å) 0. an adequate geometry optimization is essential to calculate the vibrational properties.aip. 46 parameters (CAPZ).770 ··· C-2s2 2p2 . 3(c).229 −0.750 6. A Monkhorst-Pack52 4 β (deg) −3. Norm-conserving c (Å) 7.700 rections avoid the need to use high-level quantum meth-  b(Å) 0. 3(b). (a) L-asparagine zwitterionic molecule. 3(a). (d) intermolecular tunnels in anhydrous local density approximation (LDA) using the Cerpeley-Alder.177 8.193 0. while the monoclinic unit cell of anhy- drous monoclinic L-asparagine crystals is shown in Fig. adjacent layers interact through hydrogen bonds occurring between charged groups (CO− .507 7. Within a single layer. 124511-4 Zanatta et al. scheme (GGA+TS) proposed by Tkatchenko and Scheffler48 and. the GGA-PBE functional in- LP L500 L830 GTS500 GTS830 GTS1100 Exp. L-asparagine monoclinic crystals. unit cell volume in (Å3 ).222 4. and COO− ).3 91. It was necessary to perform a DFT geom- etry optimization to evaluate both the unit cell parameters and atomic coordinates for the sake of consistency.019 ··· obtained by using the PW91 functional. and Ernzerhof (PBE)47 functional.751 6.30 91. β = 91.0543(5) Å. The gradient approximation (GGA) employed the Perdew-Burke- LDA and GGA+TS calculation results were obtained using 500.06(3) Å3 . with valence electronic configurations V (Å3 ) 288.402 −0.020 ··· each atomic species.22 3.081 5. 42 Besides.50 dispersion cor- b (Å) 6.13 were used to produce the input unit cell structure.78 45. We have also performed GGA- 1100 eV cutoff energies.30 91.051 0. Experimental lattice parameters are a = 5. Parallel layers of L-asparagine molecules form planes along the 101 direction as depicted in Fig. (c) view of two superposed 101 (ac) planes of L- tinct approaches for the exchange-correlation functional: the asparagine zwitterionic molecules.7001(5) Å. (b) anhydrous L-asparagine The DFT calculations43. which was more than enough to give a well This article is copyrighted as indicated in the article.454 5.121 0. as the electronic band structure varies appreciably when the lattice parameters and the internal atomic coordinates are changed.082 5.8 273. which belongs to the P21 space group and has Z = 2. cluding the dispersion semiempirical construct of Grimme. and unit Perdew-Zunger45. Finally.407 −0. b = 6.941 FIG. 29 Oct 2014 01:59:10 . monoclinic unit cell. and van der Waals interactions.3 277.71 electrons (36 core and 104 valence).68 −19.1 V (Å3 ) 15. intermolecular “tunnels” are present in the L-asparagine lattice structure (see Fig. 3.984 7.3 318. and to improve the accuracy of experimental data with respect to the hydrogen atom positioning.123 0. For example. J.444 0.054 pseudopotentials51 were used to replace the core electrons in c (Å) −0.070 −0.160 −0.420 ··· × 4 × 4 sampling was employed to evaluate integrals in the reciprocal space. the molecules are linked forming zigzag chains created by hydro- gen bonds involving the NH3 + group.349 −4. 124511 (2014) positions of anhydrous monoclinic L-asparagine crystals as measured by Yamada et al.0 276. The carbon backbone of the L-asparagine molecules in the crystalline phase is practically planar.706(5)◦ .050 ··· ods to describe van der Waals interactions.074 8. Chem.022 0.179 On: Wed. Lattice parameters (LP) in (Å).076 8. 140. and O-2s2 2p4 .502 0. 3(d)).172 0. Their deviations  in comparison with experimental PBE simulations modified with the extra dispersion correction data13 are also shown. for the sake of comparison. NH3 + .392 0.41.7 253.01 Å.06 87.17.980 3. Each unit cell has 140 β (deg) 88. Experimental values for the unit cell parameters from Yamada et al. The L-asparagine zwitterionic molecule is depicted in Fig. V = 273. 830.20 92. and the generalized cell angle β (deg) for the anhydrous monoclinic L-asparagine crystal.144 6. c = 8. Reuse of AIP content is subject to the terms at: http://scitation. Opto- electronic properties are also sensitive to geometry optimiza- tion. with average devi- ation from planarity being smaller than 0.

Self-consistent field convergence thresholds were: a lack of accuracy in predicting the structural parameters total energy/atom varying by less than 0. being obtained by performing single point energy unit cell structure was performed by increasing the plane.13 One can observe that the DFT-LDA calculated than electronic energies). Frac- much better gap estimates (their proposal achieves a 70% tional atomic coordinates.41.19 In order to approximately evaluate the stiffness of the an- hydrous monoclinic asparagine crystal. Chem. and then to the other two constant as well as the atomic fractional coordi- 1100 eV. A plane-wave (GGA+TS). electronic and optical properties of the anhydrous monoclinic ergy differences and electronic dielectric screening to obtain asparagine crystal to avoid extra computational costs. ues for the unit cell parameters. as it the LDA exchange-correlation functional for cutoff energies is necessary to use more k-points in the Brillouin zone (BZ) of 500 eV and 830 eV are shown in columns L500 and L830 . selected bond lengths.04 Å(b). The optimized unit cell parameters obtained using nates. pressure smaller than 0. 140.05) for a and c (b). tals).5 × 10−6 eV.1250 × 10−6 eV at correction scheme proposed by Tkatchenko and Scheffler48 most.23.66 Å. Reuse of AIP content is subject to the terms at: http://scitation.5072 Å. decrease of mean absolute errors in comparison with Kohn. It is well known quencies. The GGA+TS (GGA+Grimme) estimate for the tric function and optical absorption for polarized light along β angle was 91. Phys. with per atom) were evaluated for both the optimized LDA and a = 5. 24. After adding the extra dispersion tronic eigenenergy varying by less than 0. and atomic positions were and c = 7. b = 6. and angles for the calculated (GGA+TS and LDA) and the tional cost.49 we tronic density of states (total and partial per orbital and also obtained good estimates for the lattice parameters. the Grimme dispersion corrected GGA-PBE functional. For the sake of comparison. J. which is probably due to the dominance of intramolecular This article is copyrighted as indicated in the article.01 Å(a). All vibrational normal modes obtained for the crystal ge- lence and conduction bands were estimated by quadratic in. which der to perform the geometry optimization. with devia- GGA+TS crystals (the LDA results are omitted since the tions relative to experiment of 0. calculations after rescaling one lattice parameter and keeping wave cutoff energy from 500 eV to 830 eV. estimate the strength of interatomic interactions.5 × 10−3 Å.01 eV/Å. (Tables I–IV). Total en- IV. and smaller evolves during the geometry optimization process. with the tice parameters and unit cell volume are remarkably nice for final value selected after performing a convergence study to 830 eV. indicating that geometry optimization to a total en- that Kohn-Sham calculations tend to severely underestimate ergy minimum was reached (in a work to be published soon solid state band gaps. pure GGA functionals are able to provide imum atomic displacement below 0.17.58 showing that the GGA+TS results are in bet- oclinic L-asparagine crystals were calculated following the ter agreement with experiment than those of LDA. columns GTS500 . The BFGS a good description of hydrogen bonds. 57 below 0.aip. maximum force per atom termolecular interactions are relevant. and max. ometry with a cutoff energy of 830 eV exhibited positive fre- terpolation of the corresponding band curves. The off energy. GTS830 . In the BFGS scheme. the following is due to the LDA functional trend to overestimate interatomic convergence thresholds were considered along successive forces. we have used this cutoff energy to calculate the proach for molecules to crystals taking into account total en. this sampling was increased to 10 × 10 × 10. when running optical matrix element calculations (the matrix respectively. Nevertheless. we have we intend to present the results of the vibrational analysis for employed the -sol method proposed by Chan and Ceder.5 × 10−5 eV/ respec. 29 Oct 2014 01:59:10 .05 Å. For the optical properties cal. Downloaded to IP: 200.179 On: Wed. value (91. together with the experimental values from Ya- elements are more sensitive to the Brillouin zone sampling mada et al. than 4. compensating for the GGA ergies of 500 and 830 eV (500. b = 6. E(b/b0 ). the lattice parameters were slightly varied about their converged values. 0. STRUCTURAL PROPERTIES ergy values E(a/a0 ). tively. Using The Kohn-Sham electronic band structure and the elec. and torsion angles. unit cell parameters at 830 eV (a = 4.03 Å.941 Å. and c = 8. this is also the reason by which the LDA self-consistent field computation steps: total energy change approximation can be useful to study systems where weak in- smaller than 0. however. In contrast. In or.02 Å(c).0 Å3 for the unit cell volume variation V . and GTS1100 of Table I.54 In order to amend for that. very close to the experimental a set of chosen crystalline planes and in the case of a poly. a starting Hessian is recursively test simulations we accomplished (not shown here) suggested updated. elec. but tend to under- minimizer53 was employed to carry out the unit cell optimiza. and GGA+TS ones are considerably better). with a convergence window of 3 cycles. same scheme described in a previous work. and 1000 eV) for the underbinding effect. and some tion. 56. of L-asparagine crystals.3◦ ). angles. as well as hydrogen bond related lengths Sham gaps for over 100 compounds) with cheap computa. the results obtained using culations. 124511-5 Zanatta et al. From Table I. 830. b. bond angles.55 the infrared and Raman spectra of asparagine anhydrous crys- which extended the Delta self-consistent-field (SCF) ap. as well as the dielec.02 GPa. crystalline sample. One can note that the total energy change for E(b/b0 ) the GGA+TS exchange-correlation energy are shown in the is much smaller than those of E(a/a0 ) and E(c/c0 ). deviations a. c relative to the measurements). we have improved the estimated val- basis set represents the Kohn-Sham orbitals. The deviations relative to the X-ray measurements quality of this basis set is kept fixed as the unit cell volume are nearly 0. one can see that the lat- LDA (GGA+TS) exchange-correlation functional. Thus.883 Å) are smaller than the X-ray values (see the optimized by searching for a total energy minimum. 0. practically remaining the same for the 1100 eV cut- ensure the absence of imaginary vibrational frequencies.3◦ (92. with cutoff en. The complex dielectric function (ω) = Re()+i experimental data are included in the supplementary material Im() and the optical absorption α(ω) of anhydrous mon.02 Å (0.71◦ ). and E(c/c0 ) are depicted A convergence study of the monoclinic L-asparagine in Fig. Effective masses at the extrema of the va. 4. Lattice parameters. 124511 (2014) converged electronic structure. 3(c) are also displayed in Fig.1/2). At the closeup of the band structure around the region of the main energy band top of Fig. b/b0 . V. GGA+TS total energy E of the anhydrous monoclinic L-asparagine crystal unit cell as a function of the lattice parameter relative deviations a/a0 .org/termsconditions. A(−1/2.0). and E(−1/2. C(0. while along b hydrogen bonds and just a few co. re- spectively. Chem. covalent bonds disposed along the a and c directions (see High symmetry points (latin type.1/2. The GGA+TS electronic band structure of the anhydrous monoclinic L-asparagine crystal is shown in Fig. a closeup near the maxima.5 eV range. except for ) are indicated. for a plane-wave cutoff energy of 1100 eV. Y(0. Downloaded to IP: 200.aip. 140.1/2.0. Phys.179 On: Wed. The most important atomic orbitals contributing to the high- right panel depicting the contribution from the side chain and est valence and lowest conduction bands are also specified at some PDOS carboxyl group to each band.1/2. it would be easier to remove molecular planes along the b direction in comparison with planes along a and c. one can see the full energy range of the calcu.00) are also shown. The following set of high-symmetry points of interest was chosen: (0.5 to 12.0.1/2).0). 5. They were included since three (one) valence band maxima (conduction band minimum) occurs at α i (β).0. J. with the side panels. and β = (−0.50 eV to 12. gap. The two 101 planes shown in Fig. together with its associated partial density of states (PDOS. Electron energies were gauged to ensure that the asparagine crystals. 6. 6.17. 5.1/2). The arrangement of hydrogen bonds suggest that.0). This article is copyrighted as indicated in the article.10. except for ) and low symmetry points Fig.0. 6. valent bonds (mainly C1–C3) seem to be deformed in a re- markable way.00. α 3 = (0. Z(0.24. 3(c)).42.0. The GGA+TS calculated band structure of anhydrous monoclinic side panels). the path in the BZ used for the band structure computations is shown in Fig. as one can see from the GGA+TS band structure closeup depicted at the bottom part of Fig. D(−1/2.0.41. (greek type symbols. 5. B(−1/2.24). if the monoclinic asparagine crystal were dismantled by removing one molecular layer each time. At the bottom. For the anhydrous monoclinic L-asparagine crystal.0. Top: all bands in the −22. Usually the first BZ is sampled by calculating these eigenenergies along a path containing a selected set of high-symmetry points.00. Reuse of AIP content is subject to the terms at: http://scitation. see right FIG. 6.1/2). Other non-symmetry points as α 1 = (−0.22. FIG. bottom: highest energy valence band has its maximum at 0 eV. ELECTRONIC PROPERTIES The Kohn-Sham band structure describes the electron eigenenergies En (k) as a function of a set of quantum num- bers that form the components of a wave vector k = (k1 .0. from −22. First Brillouin zone of anhydrous monoclinic asparagine crystals. k2 .22).0. α 2 = (−0.22.00. The partial density of states displaying the contributions of the side chain (black lines) and carboxyl group (red lines) is shown at the right lated electron energies. 124511-6 Zanatta et al. b0 .00 eV.1/2. c/c0 relative to the optimal parameters a0 . and c0 . 29 Oct 2014 01:59:10 . 124511 (2014) FIG.42).0. k3 ) (n is the band number).

140.49 eV. originate exp measurements: L-alanine orthorhombic. One can see that the the types of gap (direct or indirect) and the electronic tran- HOVB orbital is really p-like and located mainly at the oxy. timate from the optical absorption data (only 50 meV larger). 6. and α2 → .59–63 Similar underestimations of the main band gap by DFT computations were previously reported main band gap reveals the most relevant electronic transitions for several molecular crystals.64 After applying the -sol ergy gap. sitions involved were not provided. and C4 atoms (sp-like orbital shapes).55 however. with EGGA g = 4.2 eV.00 eV are mainly related to C4/O3/N2. Finally.18.95 eV. as well as the theoretically cal- On the other hand.7 eV and −18.aip. 4.36 eV range. while the valence bands with lowest energies are mainly originated from s states. between −20. The closeup of the GGA+TS calculated Kohn-Sham band structure near the main band gaps (bottom part of Fig. respectively. mated gap Eg = 4.50 eV are due to N2/O3/C4 s states. O3 and along the C1–C2 and C3–C4 bonds of monoclinic α-glycine crystals19 revealed the presence of (not very pronounced in the PDOS curve). and  → Z with practi- Returning now to the top part of Fig.30 to −2.0 eV. The p orbitals. including amino acid19–22 and between the top of the valence band and the bottom of the con. C2/O1/O2. electronic transitions Z → T. cally the same energy EGGA g = 4. The bands at about direct transition.23 eV. the band sets near −20. in much better agreement with the experimental es- 5.0 eV there are seven monoclinic L-serine crystal calculated using the GGA+TS sets of flat proposed to correct this gap error. O2. to an energy gap EGGA g = 4.06 eV and a secondary transi- and a small contribution from oxygen atoms O1 and O2 (s.19 orbital localizations near the N2 and N1 atoms. A DFT simulation study gen atoms O1. Phys. isoleucine.8 and −11. in decreasing order of It is interesting to compare the optical absorption esti- exp contribution. which are in the 4. the top valence bands are dominated by p states.41. 7. and 4. The lowest energy in the −8.21 being assigned to the −9. Eg = 5. is mainly localized around the C2. respectively) shown in Fig. 124511 (2014) mainly from N1/C1/O1/O2 s orbitals and O2/O1 s and C2 p orbitals.23–4.08 eV. in this order. J.50 eV have strong contributions from O3/C4 s levels and O1/O2/C2 s levels. 5). The LUCB On the other hand.36 eV are related to the transitions α3 → .17. T → Y.0 eV being due methodology22 was EGGA+Tg S = 4. but also with sig. DNA nucleobases23 crystals.22 eV and 0 eV. The smallest gap values are both equal to 4.35 eV energy range there is a wide set gap of the anhydrous monoclinic L-aspartic acid crystal was of bands which is due to C3/O3/O1 p orbitals. 6) shows five indirect energy gaps. the band gap value we obtained was infer that the conduction bands with minima at about 4. Secondary indirect band gaps of 4. respec- tively (the α i and β points are depicted in the first Brillouin zone shown in Fig. teine crystals were predicted to have indirect energy gaps. with those close to −11. while the latter has three like character).95 eV estimated from our optical absorption measurements. 7 are clinic crystals have energy gaps Eg ∼ 5. while near estimated to be EgGGA+T S = 4.4 eV originate from C3/C1/N1 s orbitals.32 eV. Reuse of AIP content is subject to the terms at: http://scitation. on the other hand. GGA+TS calculated highest occupied valence band (HOVB) and lowest unoccupied conduction band (LUCB) orbitals. ready expected as pure DFT functionals are not able to predict excitation energies. one can see that. a nonempir- duction band. both monoclinic and orthorhombic cys- orbital. tion A → B with Eg GGA = 4. The band sets tals can be found in the literature from optical absorption at −17. 29 Oct 2014 01:59:10 . All the GGA+TS estimated indirect band gap energies.75 eV due to a S →  in- to C3/C1/C4 s and C2/N1/C4 p orbitals.30.30 eV.179 On: Wed. but details about useful to visualize these contributions.95 eV. are well below the experimental gap of 4. having also small three close indirect energy gaps. Overall.23 eV within the energy range between −1. Chem.00 eV.20 C1. and 6. α1 → . 5. 124511-7 Zanatta et al. This difference was al- FIG. while the bands The experimental gaps for the following amino acid crys- at −16. From the band structure curves and DOS plots. and C4/C3/C1 p orbitals. we correction. the two of the anhydrous monoclinic L-asparagine crystal obtained in top valence band curves originating mainly from O1/O3/O2 this work with similar data for other amino acid crystals. while the partial density of states plot displays ical scaling correction method for molecules and solids was the main atomic contributions to each band near the main en. however.52 eV. but the band curves above result from the hybridization of s and p states. β) = 4. Downloaded to IP: 200. respectively. on the other hand. Recently. corresponding to the valence band- conduction band transitions Z →  and Z → β. and valine mono- (HOVB and LUCB orbitals.00 eV there are two bands with strong contribution from indirect transition B → α 1 .27 eV.20 eV and −20. The plots of the highest occupied valence band pioneer work of Tulip and Clark17 estimated that alanine or- and the lowest unoccupied conduction band electronic states thorhombic crystals and leucine. the highest energy valence bands are culated indirect gap energy EGGA+T g S (Z → . −13. The energy gap of the anhydrous the side chain. the former with an electronic transition D → E corresponding nificant orbital lobes at N2 and O3 (sp-like orbital shapes).65 This article is copyrighted as indicated in the article. The bot- tom of the conduction bands is strongly p-like in character.

02 eV. Effective masses for electrons and holes can be estimated from band curvatures at valence band maxima and conduc- tion band minima.06.03 eV for proline. Leu. Chem.179 On: Wed. in crescent order: 3. and its two HOMO orbitals also performed DFT calculations for the isolated molecules located mainly at the carboxyl and deprotonated carboxyl re- asparagine. for histidine. Ala. from the carboxyl group to the LUMO. 124511 (2014) exp exp leucine.17. talline phase will affect significantly the electronic structure ing values (in eV) as follows: Cys (4. Phys.95) < Asp (5. As for the zwitterion aspartic acid (as in the case of lowed by valine (experimental gap larger than the gap for Gly. barely changes its HOMO using the GGA+TS exchange-correlation functional. 4. Ile. J. while their DFT-calculated estimates predict that aspartic acid crystals have an energy gap 0. Eg = 5. and tryptophan (Trp) charge carriers in a given direction and also to evaluate if the in vacuum (left) and solvated in water (right).11±0. aspartic acid. The highest HOMO-LUMO gap has two. notwithstanding the fact that the crystal is exp L-aspartic acid monoclinic. histidine has two.63 eV for a geometry optimization procedure similar to the one used for tryptophan. as their frontier orbitals do not change significantly with solvation. 8).27) < Leu (5.90). molecule in vacuum. side chain.29 eV.aip. When they latter using a continuous solvation scheme. which must. 29 Oct 2014 01:59:10 . 124511-8 Zanatta et al. exhibits HOMO and LUMO orbitals with some degree of overlap.21 and L-serine formed from molecules in the zwitterionic state. tryp- molecules were chosen in such a way to produce a sample tophan has both its HOMO and LUMO states located at the representing the different types of side chains observed in es.67 glycine. and 5. 4.04) < Gly (5. lead to larger band disper- eral. 140. sential amino acids. the 4. GGA+TS calculated HOMO and LUMO orbitals for asparagine (Asn). which also occurs to asparagine and as- partic acid. which has the smallest band gap. Val LUMO for zwitterionic aspartic acid differ from the vacuum (5. 3.02 eV.29) < Ser (5. Proline. Eg = 4. the HOMO orbital is mainly located at ing the L-serine crystal (largest experimental gap. Each optimized geometry has.68 eV uum are remarkably similar to the HOVB and LUCB orbitals (the gap of monoclinic cysteine was not measured yet).55 eV for asparagine.26 eV larger than the value for asparagine crystals.20 presented in Fig. while the experimental gaps obey the sequence (ener. (Fig. and tryptophan gions. histidine (His). in principle. while the carboxyl With the purpose to better understand the relationship side chain is twisted relative to the vacuum geometry. 8. being useful to estimate the mobility of the FIG. 4. aspartic acid (Asp). Downloaded to IP: 200. we have obtained the highest occu.95) < Ala. on the other hand. After carrying out are solvated in water. their gap figures change to 3.04 eV. degree of overlap between the HOMO and LUMO orbitals phan has a single internal hydrogen bond. and 4. pears (and the same occurs for histidine). and Val). case mainly by the absence of a significant contribution from gies in eV) Cys (4. calculated the carboxyl group.76 eV for histidine. the L-asparagine crystal. The HOMO and < Asp (4.23) in comparison with the anhydrous crystal. leading to the second smallest HOMO-LUMO band gap. 4. These and LUMO shapes as we switch from vacuum to water. Two molecular states were assessed: the The HOMO-LUMO energy gaps calculated for the amino neutral state in vacuum and the zwitterionic state in water acid molecules in vacuum were. groups and does not form a zwitterion when solvated). a trend which reverses the order of molecular HOMO-LUMO gaps. proline. Reuse of AIP content is subject to the terms at: http://scitation. fol. in gen. Besides.00 eV for histidine. proline (Pro). The HOMO and LUMO orbitals for asparagine in vac- exp 5. on the other hand. For the aspartic acid There are two disagreements between these sequences involv. and trypto.24 eV for aspartic acid. both molecular orbital (LUMO) for each molecular configuration. 8. Proline.02) < Val the ammonium group (amine protonated) to the HOMO and (5.75) < Gly (4.67 eV (except for proline. which has its amine bound to two alkyl for tryptophan. 4. The theoretically calculated 22 to indicate that the insertion of water molecules in the crys- energy gaps of these amino acids can be ordered by increas.52) < Asn (4. Thus. a set of stabilizing internal hydrogen bonds: asparagine sion in tryptophan crystals. we have water) located at its side chain. proline has none. intermolecular interactions in the crystal are strong enough to This article is copyrighted as indicated in the article. It is also worth to note that as- paragine and aspartic acid crystals have very close experimen- tal band gaps. the ammonium contribution to the HOMO disap- while the theoretical gap is smaller).68) < Asn (4. Histi- between the band gaps of these amino acid crystals and the dine has its two LUMO orbitals (in vacuum and solvated in electronic structure of each amino acid molecule.41. asparagine).61 eV for asparagine. by the way. for this amino acid. 7.19 cysteine orthorhombic. Ile. histidine. Eg = 5. seems to be related with the small terion state. aspartic acid has two in vacuum and one in the zwit. while the LUMO is concentrated at the gap smaller than those for Gly.0). Eg = 5.49) < Ser (4.90 eV. Leu.97 eV for eV for aspartic acid. it also has a very small variation in the HOMO-LUMO gap as we switch from vacuum to water. This seems exp monoclinic. the HOMO and LUMO orbitals are located at the side chain both shown in Fig. one must conclude that intermolecular inter- action effects cannot be ignored in order to explain the elec- tronic properties of amino acid crystals. as a de- scription based only in the analysis of the isolated molecules is clearly not enough to explain the experimentally observed gap differences.66 valine. Eg = 5. In the pied molecular orbital (HOMO) and the lowest unoccupied case of tryptophan. indole side chain.11) < Ala (5.

while the H 1s This article is copyrighted as indicated in the article. The effective  for the  − C direction and the smallest one (2. however. 124511-9 Zanatta et al. depicting the relative contributions of all carbon. 9. as the bands for both gens at the carboxyl group and side chain. Looking just to the band widths. indicates that the inter- critical point. 11. as well as the C 2s. Gray (black) band widths correspond to the band along the masses were obtained for them along a selected set of direc- parallel (perpendicular) direction. 124511 (2014) FIG. Phys. 11 and 12. Reuse of AIP content is subject to the terms at: http://scitation. we have first evaluated is strong enough to allow for the usefulness of the electronic the effective masses for the uppermost valence band. 3(c)). The values anhydrous asparagine crystals is shown in Fig. tions. nitrogen. while to effective masses of about 3. and effective shown in Fig.59 m0 the bands between −9. 140. top of the valence band. as the conduction band minimum β are indicated. parallel and perpendicular effective masses have nearly the same range of energy variation.79 m0 (along  − B). and N 2p ones. dispersion of the band curves. and hydrogen atoms to the total DOS of the asparagine along the 101 direction (see Fig. For electrons. For the perpendicular di. with the largest effective mass (4. the smaller (larger) the effective mass will be. at the Z point (hole effective masses) and for the lowermost Additional details on the atomic and functional group conduction band. with corresponding hole and valence VB and conduction band CB widths (below). other hand.0 eV are mainly due to (β − β ).62 m0 ) at mass calculation procedure is easy to implement: one must  along  − Z. As a rule of thumb. leading C 2p states above −3. together with the band widths in the neighborhood see from it. are shown in Fig. contribute significantly to the conduction bands which points to the difficulty of moving the charge carriers above 6. although not as large as it oc- one can say that the larger (smaller) the band width near the curs for covalent inorganic crystals.7 eV and by O 2p states below. on the lence bands between −5. they are always mensurable. O 2p gives the most significant contribution to the of these points. there is a smaller degree of variation. In the case of electrons.4 eV are dominated by other hand. which suggests that a wide gap semiconductor the N 2p orbitals. affect the electronic structure and produce a significant dif. however.0 eV and −2. GGA+TS estimated electron and hole effective masses (in free elec. where m0 is the free electron masses. centered at the β point.63 m0 (Z −Z ) and 4. The valence band maxima α i and performed at the valence maximum and conduction band minimum along di- rections parallel and perpendicular to the molecular layers of asparagine. we see that the hole and electron effective masses part of the bottom of the conduction band.179 On: Wed. lence band has a strong contribution from both the oxy- one cannot predict this result. on the are larger than 10 m0 . ing at the  point along the k-axis. 9.17. The per orbital per atom partial density of tom of Fig. each one starting or end- tron mass units. the band curves have larger J. while the C 2p levels originate most rections. The fittings were (electron) effective masses. in Figs. and some zone and project it along a chosen path. centered band structure picture.33 m0 ) being observed at ference with respect to pure molecular states. effective masses are somewhat large (always larger than the spect to the wavevector at a critical point in the first Brillouin free electron mass). ranging from 1. H 1s states.60 m0 (along the Z −  and D − α 1 −  paths) to 7.2 eV. one can see that the top va- these 101 molecular layers.aip. For holes. ermost) valence (conduction) bands. 6). Chem. action between asparagine molecules in the monoclinic phase For the anhydrous asparagine crystal. GGA+TS estimated electron and hole effective masses (free elec- tron mass units) for the anhydrous monoclinic asparagine crystal. As one can obtained. 5.0 eV and −5. which is situated contributions to the density of electronic states can be seen along the linear path connecting the  and B points (see bot. Two directions were selected for each point: states. there is a very strong anisotropy in effec- tive mass values. Notwithstanding the fact that the calculated take the inverse of the second derivative of the energy with re. mo ) for the anhydrous monoclinic asparagine crystal (above).41. oxy- parallel () and perpendicular (⊥) to the molecular planes of gen. Figure 10 presents five panels with the uppermost (low- FIG. Va- from one molecular layer to the next. Downloaded to IP: 200. behavior can be achieved for charge carriers moving within Looking now to Fig. 12. C 2p. 10. Parabolic fittings are also shown. 29 Oct 2014 01:59:10 .

29 ing of amino acid molecules from internal hydrogen bonds.5 eV (mainly ni. on the other hand.10 transfer in amino acid crystals can play a role in the unlock- C4 0.23 H3 0.09 Carb.08 H1 0. 78 as Hirshfeld atoms in general resemble the (about 5. and H 1s deep valence levels can be as. can be amended A set of O 2s. sion of Fukui functions.3 eV (carbon). O1 − 0.78 which has signed to the carboxyl group near −20. using the iterative Hirshfeld charge technique. Phys. The bottom information related to the formation of chemical bonds be- of the conduction band.82 trogen).77. 11.0 eV been successfully applied to the solid state81 and the discus- (mainly oxygen).03 H8 0.74 Besides.16 N2 − 0. as FIG.0 eV comes electrostatic potentials. In Table II. Among several methods of charge partition- This article is copyrighted as indicated in the article.21 HPA produces im- proved Fukui function indices69–71 capable of predicting re- activity trends within a molecule better than Mulliken pop- ulation analysis. neutral atoms. black) orbitals. N 2s. J.02 N1 − 0.10 Intermolecular interactions. Hirshfeld atomic charges (in e units) for the L-asparagine molecule in the anhydrous monoclinic Asn crystal as calculated at the state located mostly at the side chain. ing available in the literature. from the carbon atoms at the carboxyl group.4 eV (nitrogen). and charge C3 − 0. 80 This limitation. as can also be seen from Fig. for energies a bit larger be too small. Hirshfeld population analysis (HPA)68 provides one of the most promising approaches. N. with a smaller contri- GGA+TS level. COOH lateral chain.1 eV (mainly oxygen). and H: s (dotted. bution from the carboxyl region.79. 12. (in units of the fundamental charge e) of the individual atoms One can infer from these results that the main indirect gap transition occurs between a valence electronic state with localization at the carboxyl and side chain and a conduction TABLE II. it is interesting to estimate how changes in the O2 − 0. to the amine group at −17. and to the side chain at − 1–8 therein).01 hydrogen bond patterns can influence the electrical charge O3 − 0. Reuse of AIP content is subject to the terms at: http://scitation. 76 However. and amine groups: s (dotted.aip. − 0.17. charged states. red) and p (solid.11 C2 0. Downloaded to IP: 200.22 H4 0. we present the GGA+TS Hirshfeld charges −16. however. − 0. O. 29 Oct 2014 01:59:10 .72 natural bond orbital analysis. Anhydrous asparagine monoclinic crystal GGA+TS partial den- sities of states for the carboxyl. HPA minimizes the loss of from the side chain.17 H2 0. black) orbitals.07 H6 0. 7.10 Am. and −13. 124511-10 Zanatta et al. originates from the tween atoms in a molecule.58 C1 0. Anhydrous asparagine monoclinic crystal GGA+TS partial densi- ties of states for C. we have pointed out in another paper. its values tend to carbon atoms at the side chain and.15 H7 0.179 On: Wed.04 S.4 eV and −18.24 Consequently. red) and p (solid. More details on the specific contributions of each atom Atom HGGA + TS Atom HGGA + TS Atom HGGA + TS of asparagine can be found in the supplementary material (Figs. Chem.0 eV).22 H5 0. followed by the amine group. 0.04 ··· ··· of each atom.C.41.75.73 and fitted contribution for the conduction bands above 6. 124511 (2014) FIG. 140.

72 eV (the shift for the -sol estimate would be almost the the local pKa of amino acids in proteins to the charge transfer. 124511-11 Zanatta et al. if we sup.40 One can see that O1.aip.95 eV while the transfer processes occurring at their side chains. like the C3 atom of the side chain. the study of the structural and electronic properties of amino acid crystals is the first step to be taken. and −0. eV (about −4%).29 e.11 eV. Chem. which are GGA+TS computations predicted a minimal indirect band affected by the particular combination of hydrogen bonds and gap of 4. The carboxyl. amine. and 02̄3.17. Downloaded to IP: 200. Phys. there is a relationship between charge redistribution erties (absorption. and side chain groups have Hirshfeld GGA+TS calculated charges of −0. Comparison between the optical absorption of the anhydrous mon- character of the zwitterionic L-asparagine molecules in the oclinic asparagine measured with nonpolarized incident radiation at 300 K (solid line) and the GGA+TS calculated optical absorption for a polycrys- anhydrous monoclinic crystal. However. Eexp = 5.52 eV. we have calculated the optical prop- sides. −0.24 e.72 eV or −15%. For the seems reasonable to consider that the folded state of proteins L-asparagine crystal. Eexp = 4. the GGA+TS scissor curve is in good agreement with the gether with the charge transfer to the asparagine side chain as measured data.18–22 VI.22. with 001. clinic asparagine crystal for light polarized along the directions 100. this trend is also verified as the optical (or their structure-activity relationship) is related to charge measurements pointed to a band gap of 4. talline sample with scissor shift (blue dotted line) and without scissor shift One can argue that intermolecular interactions involving (red dashed line). at their side chains. hydrogen bonds are somehow responsible for the small neg- ative charge of the side chain of L-asparagine molecules in anhydrous monoclinic crystals.179 On: Wed. together with the experimental result. Reuse of AIP content is subject to the terms at: http://scitation. They were calculated using the HPA scheme available in the CASTEP code. respectively).16 eV (about −3%).89 eV. which exhibits a small negative Hirsh- feld atomic charge (−0. For the α-glycine crystal. 13. we have found Eexp = 5. the crystal field connection with the as.01 e. a difference of 0.68 eV and the smallest calculated gap was indirect. same. with −0. the theoretical estimate being smaller than experiment by only 0.23. Under such viewpoint. EDFT = 4. which reveals the dipolar FIG. The N2 nitrogen atom belonging to the side chain is negatively charged (−0. to.23 eV.53 eV or −11% smaller than experiment). light with polarization and for a polycrystalline sample us- plex pattern of the spatially dependent complex function of ing a scissors operator to shift up the theoretical band gap by proteins. the DFT calculated energy band gaps for monoclinic α-glycine19 and orthorhombic cysteine20 were close to the values obtained from optical absorption measurements. while for an.49 eV FIG. out the scissor operator in the case of a polycrystal are shown Within this picture. As a matter of fact.11 eV and an indirect DFT gap EDFT = 4. respectively.15 e). dielectric function) for the case of incident processes due to intermolecular interactions and the com. 101. 0. Considering that DFT calculations crystals as it occurs for the isolated amino acid species and typically underestimate band gaps by 50%.02 eV and an indirect gap EDFT = 4. account this difference. For cysteine. suggest Figure 14 depicts the optical absorption obtained from the important role of hydrogen bonds on the protein folding the GGA+TS scissors electronic structure in the case of in- route and on the inhomogeneous dielectric function. 0.74 eV (0. hydrous monoclinic L-serine crystals. Be. obtained by the GGA+TS calculations (see Table II). The optical absorption for the polycrystal is also shown. in Fig.22 e.77 eV). 29 Oct 2014 01:59:10 .83–86 It is not less important to associate changes in 0. a difference of 0. for monoclinic anhydrous L-aspartic acid crystals we have ob- tained Eexp = 5. 010.08 e). and −0.37 eV or −7% pose that charged side chains are also present in all amino acid smaller than experiment).41. 124511 (2014) and functional groups (carboxyl. 140. 14. further studies are necessary to fully unveil the role of hydro- gen bond unlocking in proteins. our calculated fig- for polypeptides interacting in aqueous environment. 13. Taking into van der Waals forces related to their peptidic backbone. On the other hand. OPTICAL PROPERTIES In previous works. GGA+TS calculated optical absorption of the anhydrous mono- (0. amine. as well as the N1 at the amine group. O2. DFT predicting a direct gap EDFT = 4. The optical absorption curves with and with- affected by the hydrogen bond pattern. This article is copyrighted as indicated in the article. side chain) in a sin- gle asparagine molecule belonging to the anhydrous Asn monoclinic crystalline phase. see. then it ures are surprisingly close to the experimental data. 1). As one can paragine hydrogen bond unlocking process (see Fig. O3 are the most negatively charged atomic species (Hirshfeld charges of −0.07 e.

for light polarized along 02̄3. Real (solid black line) and imaginary (dotted red line) components of the GGA+TS calculated dielectric function of the anhydrous monoclinic optical absorption of its powder was measured and its struc- asparagine crystal for light polarized along the directions 100. The calculated unit cell param- below 8.00 eV. anisotropic optically.3 eV. The absorption curves reveal that sulator depending on the effective mass-related electrical mo- anhydrous monoclinic L-asparagine crystals are remarkably bility of their charge carriers.020 Å.30 for ener- gies between 6. 124511 (2014) ization. becoming negative at 14. C2 p carboxyl analysis of the real part  1 .org/termsconditions. the main gap in- tion is proportional to the optical absorption we have dis. tural. Finally. The FIG. in Fig. histidine. only the water solvated form is zwitterionic as in the crystal.95 eV was estimated from the optical absorption data.0 eV has a erties (absorption and dielectric function) for the L-asparagine pronounced peak at about 7.0–6. observed band gap differences among amino acid crystals. After tions of Fig.022 single absorption peak at nearly 6. for energies try optimization procedure. Chem. (ω) =  1 (ω) transitions. with a larger number of pronounced maxima and min.15) in the 2. This article is copyrighted as indicated in the article. The imaginary part  2 of the dielectric func. Downloaded to IP: 200.3 In particular. suggesting that L-asparagine cident light polarized along a chosen set of directions (100. and optical prop- inside the unit cell. the direction of the hydrogen bond O2 · · ·N1 H7 between the The electronic band structure.41. amine and carboxyl groups of neighbor asparagine molecules carrier effective masses. For the 101 direction. tured. Reuse of AIP content is subject to the terms at: http://scitation.0 eV only.23 eV indirect band gap for both the Z → . applying the -sol gap correction scheme.32 eV (α 1 → ). 14. and 02̄3.9 eV. 15 we see the GGA+TS calculated real ited a 4. In the case of 010 polar. almost matching the experimental gap esti- cussed in the previous paragraph.  1 is practically constant (approximately 2. the optical absorption for smaller as the values obtained using the GGA+TS approach.051 Å. and optical properties were computed using 101. creases to 5. One can note that  1 becomes negative in the 7. the HOVB and LUCB orbitals in L-asparagine eV. 4. β and imaginary parts of the dielectric function. paragine and other four amino acids (aspartic acid.0 eV and 7.9 eV. The  1 curve in the 101 polarization plot has a maximum at 5. (α 3 → ). tal energy was achieved. following the same scheme of polarization direc. CONCLUSIONS The anhydrous monoclinic L-asparagine crystal was studied in this work as a new contribution to obtain a complete picture of the properties of amino acids in the solid state. displays a set of very pronounced peaks at eters showed very small deviations in comparison with X-ray 6.3 eV and above 16. VII. the absorption curve below 8. and tryptophan) reinforced the need to take into ac- ima in comparison with the 010 case. electronic. b = 0. The unit energies resembles the 100 curve with some degree of atten. For the 100 polarization count intermolecular interactions to describe adequately the we have a pronounced maximum for  1 at 5. 101.aip.179 On: Wed. which is parallel to the molecu. β = −0.1 eV. Unit cell parameters calculated range. crystals can behave as a wide band gap semiconductor or in- 010. Å. orbitals contributed most significantly to the highest valence tric function is very polarization sensitive. J. notwithstanding the fact that with respect to the electric field). assuming negative values for energies larger than 16. which corresponds to ter revealed that the unit cell is less stiff along the b direction. 15.5 eV energy range. partial density of states. functional. and 4.17.1 eV–7. For example.0 eV.0 eV and looks very similar to the crystal were obtained after the unit cell with minimal to- absorption curve for the 001 polarization. 3(d)). The O 2p carboxyl and the C4 side chain. In the case of 02̄3 polarization. The dielectric function curves for the 100 ison between the HOMO-LUMO gaps between molecular as- and 101 polarization directions are considerably more struc. as well as  1 for a polycrystalline sample. An indirect band gap of 4.  1 looks very similar to the 001 curve. and for 010 polariza. cell total energy variation as a function of the lattice parame- uation. A compar- optical absorption. 010. and three close indirect band gaps of 4.9 eV and a sec.0 eV (the negative sign means HOMO and LUMO states of L-asparagine in vacuum than that the molecular induced dipoles are oscillating out of phase those of L-asparagine in water. and 02̄3). see Fig. 124511-12 Zanatta et al. 29 Oct 2014 01:59:10 .7 eV. using the Grimme dispersion correction scheme were as good lar layers of L-asparagine. Phys.1 eV. increases slightly to 3. 001. 001. a convergence spectrum for polarization along 100 (which is parallel to the study was carried out to ensure the quality of the geome- crystalline intramolecular tunnels. proline. the optical absorption As for the DFT-GGA+TS calculations. the real part of dielec. 140. c = 0. Hirshfeld charges. when a 830 eV cutoff energy for the plane tion the optical absorption is very small in the same energy wave basis set was employed.9 eV and a minimum at 7.30 eV + i 2 (ω).420◦ . so we focus now on the mate. as for the 100 case. followed by a minimum at 7. As expected. as occurred for the and lowest conduction energy bands.6 crystals exhibit a structure which resembles more closely the eV energy range. The real part of the di- electric function for 001 polarization has its main maximum at 8.36 eV (α 2 → ). in this order. and above 16.1 eV. and then falls off. while for the 001 polarization there is a diffraction data: a = 0. ondary maximum at 6. Its electronic band structure exhib- Finally. The dielectric function components for the polycrystal are also the DFT-GGA+TS dispersion corrected exchange-correlation shown.5 eV and 9.

(2005). Alpert. 1218 (2010). Chem. J. 98. A. V. Parpura. Hannewald. D. Rev. 5384 (2006). Dutta. P. T. J. Phys. Rep. Yokoyama. R. K. Auwärter.A.179 On: Wed.S. Phys. P.C. and W. and Z. Lett. and J. L. L. M. N. bles depicting the atomic fractional coordinates. Chidambaram. and R.A. Phys. (2008). 136. 8 P. W. P. (2006). Comput. J. and H3. Dell’Angela. Kohn. Monti. Heine. J. Marschall. Proc. and O3 (side chain) atoms are the most neg. K. Clark. Catak. Acta Crystallogr. Silva. Jpn. J. Comput. 14. B 13. 77. For electrons. Monkhorst and J. the charge population analysis. Rev. Phys. M. Appl. J. L. R. 13. V. F. Probert. 8939 (2006). Downloaded to IP: 200. K. National Research Council (CNPq). M.W. Weber-Bargioni. Raleigh. Sales.009381 (2011). 862 (1961). Lett. Hohenberg and W. K. Qteish. A. Hamilton. N. U. Lindan. B 28. Yamada. F. W. Oxford Master Series in Condensed 1 J. Robinson and A. Rev.. 36 M. D. M. and W. M. as well as figures displaying the partial densities Reire. atively charged. Chem. 4174 (2005). and S. Cavada. E. 131. Phys. J. W. B 77. 7817 (2005). M. and R. 2001). Pena. 45. and GGA+TS approaches. Maia. M. Pickard. 20 J. 5221 (2013). J. J. P. S. it seems that for most di. the opti. V. acknowledge the financial support received during the de. A. Phys. De Lima Filho. N. and D. Allegretti. Perdew and Y. Albuquerque. N. Chou. Schmidt. N. Perdew. N. 3865 (1996). 9 M. E. Finally. the α 1 point along the D −  path) to 14. CrystEngComm 14. M. Caetano. Pfrommer. Dovesi. Phys. F. O111. J. 32 S. and 41 S. Chem. McKerrow and A. S.S. 20356 (2012).G. A. Persson. Acta Crys. Pfeiffer. Soc. C. G. Matter. A. E. 34 M. Gale. Matter Physics (Oxford University Press. velopment of this work from the Brazilian Research Agency 35 M. and L. D. 304283/2010-0 and 474734/2011-0. 208 from 2. Chem. Lett. T. Pack. effective mass values pointed to A. Natl. Monard. Demichelis. Burke. J. 42 R. Rev. K. 102. Bauer. H. and V. P. Acad. S. J. and D. 37 V. Prog. 14 G. 16 J. A. 13 K. Appl. Jr. 19. 46 J. Sci. S. Maes. W. 38 H. of states calculated using the GGA+TS exchange-correlation functional. S. and M. E. Phys. 10173 (2009). Maia. and C. Phys. L. Chem. C 116.N. A. 13244 (1992). G. B 23. F.4 m0 (at β. the perpendicular to the L-asparagine 101 planes). L. M. (1993). De Oliveira. and V. F. E 63. Ruiz-López. Tkatchenko and M. Bechstedt. Chem. and R. 12658 (2012). Dunkelberger. Lehmann. Silva. Lopez. Sales. 27 S. Cellular Proteom. J. 11 C. Trout. J. S. Fulco. and would like to 33 M. C. Varela. Optical Properties of Solids. Ladeira. Phys. 131. Ortmann. 175101 (2011). Wang. J. Hasnip. L. Bechstedt. 12409 (2001). 2 N. Z. Oda and T. Phys. anisotropic hole effective masses ranging from 1. Fernandez. 40 D. Hao. L.1 m0 (at Z along a Caetano. G. Marek.S. J. 26 M. Chem. Koetzle. 15 M. S. Cândido-Júnior. M. Phys. Alves. Wöll. B. Nano 7. Clark. Rev. Sec. Ortmann. C2 atoms (side chain and carboxyl groups). M. Medeiros. I. J. Soc. W. Mol. Lett. Rev. Caetano. Pinheiro. Nat. Ernzerhof. 1772 (2005). Fulco. 153 50 J. R. Phys. Phys. J. S. 95. K. C. and E. S. Humblot. B. U. Li. V. Baldwin. V. Kohn and L. Phys. Sariciftci. V. A. are senior researchers from the Brazilian 115. Albuquerque. De Lima-Neto. behave as a semiconductor. 233 (1997). S. 10 B. and S. W. T. Payne. G.: THEOCHEM 719. V. Acta Crystallogr. Reichert. Phys. J. Cabezas. Phys. Cryst. Scheffler. Am. 7 S. J. Robinson. 1787 (2006). Ceperley and B. 55 M. R. along (2011). 39 A. Cossaro. followed by H6. F. A 112. and M. Chen. and J. Chan and G. 223112 (2010). Kim. Phys. Flores. E. V. 4 M.17. Kravchuk. 195117 (2005). A. From and E. Oliveira. calculated carrier effective masses. E. C. L. C V. Sci. Hashizume. Nature (London) 192. B rections the anhydrous monoclinic L-asparagine crystals can 86. Phys. Leite. followed by the N2 atom and the C3 atom. received financial support from CNPq Projects Nos. N. Sikka. 244. 186101 Sec. Sec. Verbist. Langmuir ACKNOWLEDGMENTS 27. Fischer. Irimia-Vladu. Rev. B 47. Naitabdi and V. Nefedov. Selvaraj. Ortmann. Lett. A. 2393 (2011). Fan. M. Z. G. 47 J. Nakayama. 10. M. and M. C. Rev. Catak. Murugan. Flores. direction perpendicular to the planes of L-asparagine approx. Chem. Science 183. Payne. Costa. 165–166. Ceder. Albuquerque. L. F. Wang and W. 124511-13 Zanatta et al. Barth. (2013). Cao. Phys. N. Murphy. R. 105. it was inferred that the O1. which has large ef. G. V. Marschall. J. and hydrogen bond lengths for L-asparagine crystals in both the LDA 18 E. Lin. C. and M. 627 (2005). Kartha and A. Farias. H7.: Condens. Rev. P. varying D. A. 56 F. A. 544 (2010). Katayama. Caetano. M. Alder. Pharm. Zunger. Fox. Zanni. 23 J. O. J. 073005 (2009). 195201 (2012). J. the effective mass is more isotropic. G. 3 E. Costa. 205101 B 28. C. Papageorgiou. D. L. Rev. G. Freire. J. F. P. 512. E. Hong. and F. From the 21 A. Payne. Schmidt. Willett.1063/1. Phys. while the largest positive charge was observed for the C4 and Acad. R. C. W. C 117. N. D. Boeckx and G. J. Phys. and U. Proc. Y. Farias. F. 5048 (1981). 5 B. E. Aviyente. Carravetta. S. Rev. 24 F. (2011). G. F. Rev. Z. M. Chem. B. Lett. 566 (1980). Phys. fective masses and then suggests an insulator character. A 110. 3006 (1972). K. Morgante. Bezerra. Robinson. L. M. Chem. N. 44 W. and E. bond lengths.60 m0 (at 1095 (2005). B 73. Biochemistry 45. 2793 port between parallel molecular planes. with more structured curves for the 100 and 001 polarization 29 S. Lett. 27. Proc. W. o3802 (2007). J. and J. Peters and B. and M. Jeon. 196403 (2010). P. Rev. 52 H. L. J. B. M. Growth Des. Chem. R. L. U. F. 4636 (2011). Freire. J. Mol. Grimme. Segall. and H. Kim. A. E. Caetano. Phys. Forster. cal properties (absorption and dielectric function) displayed 28 J. Louie. 573925/2008-9. 1540 O2 (carboxyl). 48 A. Tulip and S. Azevedo. B 45. Phys. Phys. Phys. Buchanan. 772. S. K. 8752 (2008). Sales. Cohen. Bavdek. Scolfaro. S. 97. S. 27. 102. Azevedo. Phys. 44 (2012). Lett. Mater. Chem. Chem. and F. Sales.41. gles. Cavada. Rev. E. D. Raiteri. Stroscio and M. Freire. Vattuone. Nakayama. Struct. along  − Z) up to 10. W. R. 51 J. ACS Nano 4. S. Am. de Oliveira. J. Appl. 1350 CNPq-INCT-Nano(Bio)Simes Project No. S. 62 (2012). Y. Albuquerque. and H. Côté. Cvetko. and S. R. Leite imately aligned to the 101 direction) free electron masses. Raval. K. 29 Oct 2014 01:59:10 . F. W. 85 (1974). F. P. H. Chem. 48. T. Natl. Monard. Ramanadham. Ruiz-López. F. 53 B. Sze. V. Rev. 115104 (2008). Chem. A. Phys. and L.aip. Bechstedt. Smerieri. Sham. Phys. T. Maia. F. F. 134. B864 (1964). 43 P. L. G. West. Bezerra. Shimizu. M. 143 (2012). Res. A. Rev. E. B. Ågren. 12 A.4869179 for ta- tallogr. F. B. 22 S. L. H8 (amine group hydrogens). Mata. torsion an- 17 P. P. Reuse of AIP content is subject to the terms at: http://scitation. Freire. Jung. 140. Bezerra. IEEE 93. B. Fernadez. L. S. Chem. D. 5188 (1976). 45 D. Sci. 21. Caetano. A. K. M. D. J. Ren. B 112. and S. Commun. Pinheiro. Phys. P.62 m0 (at . 59 (2007). J. Chem. A 116. S. 31 A. 54 C. Reichert. Moreira. S. the exception being the trans. W. 25 R. 134. Maia. 49 S. G. J. B. Caetano. A. 6 S. a very strong anisotropy to the incidence of polarized light. Huang. 5934 (2012). Lin. C. M. 597 (1983). 3000 (1972). W. 58 See supplementary material at http://dx. Freire. 51.F. Surf. S. Alonso. 107 (1956). dos Santos. D. J. R. J. L. This article is copyrighted as indicated in the article. 11702 (2012). Perdew and A. Klappenberger. C. directions. J. B 71. Biophys. Y. S. and M. 45. Proc. A1133 (1965). Pickett. 124511 (2014) On the other hand. 57 F. D. N. De Vries. Oda and T. AIP Conf. 19 M. Diller. M. 30 M.doi. 435. F. M. A. Phys. E. Aviyente. F. Schiffrin. Barth. Savio. J. J. 8354 (2006). F. S. 140. L. J. 2717 (2002). P. Manning. Costa. M. S. Lett.

Chem. 3883 (1985). and R. (2000). Pal. N. Chem. Roy. Kar. Am. 68 F. M. 62 L. 45. 71 R. 3957 Gopalakrishnan. Theor. Phys. and P. 13. 8236 (1999). 026403 (2011).A. 102. 60 J. J. P. Rev. Phys. 9359 (2002). Vijayan. G. Phys. Chakravorty. 7211 (1980). Kinkar Roy. Foster and F. J. Sham and M. Rajasekaran. Roy.179 On: Wed. 69 R. H. V. K. P. Chem. Sukhomlinov. 81 T. This article is copyrighted as indicated in the article. W. 116. and S. C. J. J. Baker. E. 2901 (2001). V.41. Soc. Hu. P. S. Hirao. Phys. J. 2075 73 J. Seidl. Phys. S. Mori-Sánchez. Lett. Palanichamy. Cryst. J. R. 3764 (1996). C. S. (2005). Chem. G. Mori-Sánchez. J. Chem. 97. Harris. Bultinck. 74 R. Phys. B 77. S. 319 63 A. W. Ayers. Chim. Proc. 84 G. (2003). Mulliken. Phys. and W. Weinhold. 64 X. 144111 (2007). W. and W. 132. 65 N. A 109. Cohen. B 75 P. Phys. 115123 (1992). 70 (2010). Phys. Theor. Phys. Ayers. Phys. Phys. F. Chem. 8879 61 L. Yang. 235103 (2010). U. Chem. Chem. M. Downloaded to IP: 200. Hirao. 86 X. 79 P. 83 W. R. Phys. J. Lett. B 32. Mater. 51. 110. 72 R. Ayers. W. Guest. and 66 S. Ramesh Babu. Nalewajski and R. Phys. J. 4049 (1984). Bultinck. Phys. K. 51. Tomasi. Levy. Acc. P. Rev. J. Schlüter. J. Verstraelen. Kar. Rev. 85 A. R. Parr. Majewski. J. 8731 53. S. Chem. Phys. T. 370 (2006). and J. Bonaccorsi. 80 R. Parr. Chem. G. Sci. 107. 490 (2012). 70 R. Acta 83. 76 R. 034102 (2007). Yang. Perdew and M. Phys. 82 P. Smirnov. 2441 (2006). J. 127. S. Sham and M. Yang. J. (2008). G. R. Soc. Hirshfeld. Parr and W. 140. J. P. A. Krishnamurty. Chem. J. Growth Des. J. Chem. C. 23. Res. Nalewajski. Chem. Phys. S. 115. Technol. Lett. Kortemme. 116. Rev. Phys. C 116. 115. Rev. 6286 (2011). P. Acta 44. 133. and J.aip. A. 77 E. Cashman.S. Chem. Chem. A. C. S. 1833 (1955). Davidson and S. and S. B 107. 78 P. 5270 (1970). Chem. 29 Oct 2014 01:59:10 . Zheng. Van Speybroeck. K. Bhagavannarayana. 129 (1977). Chim. and R. J. Waroquier. 124511 (2014) 59 A. V. Pal. 52. F. (2002). and R. 106. Chem. 1888 (1983). 67 S. Plotkin. and R. A. P. Ayers. Natl. Carbó-Dorca. Fias. S. Carbó-Dorca. J. and M. Am. Rev. J. Morrison. Ayers. P.17. Chem. 1055 (2012). 124511-14 Zanatta et al. 1884 (1983). Moitra and T. Van Alsenoy. Görling. Phys. Chem. Phys. Harding. Cohen. Van Alsenoy. Phys. 126. Ramasamy. K. Acad. Scrocco. and D. X. Adhikari and T. Cryst. Patargias. 6. Schlüter. and K. Morozov. Song. Theor. Reuse of AIP content is subject to the terms at: http://scitation. Vogl. Levy.