This journal is c the Owner Societies 2012 Phys. Chem. Chem. Phys.

Cite this: DOI: 10.1039/c2cp43884d

Glycine conformers: a never-ending story?†

Vincenzo Barone,*a Malgorzata Biczysko,b Julien Bloinoac and Cristina Puzzarinid

The structure and vibrational spectra of a marginally stable con-

former of glycine (usually referred to as VIp or ttc) recently

detected in low-temperature matrices have been characterized

by a state-of-the-art computational approach allowing an overall

quality for bond distances, rotational constants, conformational

enthalpies and vibrational frequencies well within the chemical

accuracy. The high accuracy of the computational results allows us

to draw a fully consistent interpretation of the available experi-

mental data and to obtain a more complete characterization of an

elusive glycine conformer.

In 2012, one might think that the structure and properties of amolecule as simple as glycine have been established withoutambiguities, especially taking into account that it is quite stablein the gas phase and represents one of the fundamentalbiomolecule building blocks.1–3 However, this is not actuallythe case as demonstrated by the number of experimental andtheoretical papers published in the last couple of years report-ing new results about elusive conformers either predicted bytheory and escaping unambiguous experimental characteriza-tion4,5 or, conversely, barely stable according to theory, butactually identified by suitable spectroscopic experiments.6,7 Inparticular, the so-called VIp/ttc conformer (see Fig. 1) of glycine

and its trideuterated [ND2,OD] isotopologue, glycine-N,N,O-d3,have been recently prepared and characterized in low-tempera-ture matrices,6,7 but their structural and spectroscopic proper-ties have never been investigated by means of high-levelcomputational approaches in view of the predicted low stabi-lity.8,9 As a matter of fact, unstable conformers can be actuallyeasier to characterize than their more stable counterparts dueto longer lifetimes resulting from higher barriers of intercon-version to the absolute energy minimum, the Ip/ttt conformer,and/or from less effective tunneling. As an illustration of thisobservation we can mention the case of the relatively stableIIIp/tct or IVn/gtt conformers, for which the experimentalcharacterization faced intrinsic difficulties (see ref. 3–6 and 10).On this matter, the purpose of the present communication is toanalyze the glycine VIp/ttc conformer and its trideuteratedisotopologue by means of the state-of-the-art integrated approachwe recently applied with success to uracil and glycine.10–14

The aim here is to derive structural, thermodynamic, andspectroscopic properties with an overall accuracy of about, ifnot better than, 0.001 Å, 20 MHz, 1 kJ mol�1, and 10 cm�1 forbond distances, rotational constants, conformational enthal-pies (i.e., enthalpy differences between conformers), and vibra-tional frequencies, respectively. This high accuracy can bereached using composite schemes based on coupled-cluster(CC) computations (at the CC singles and doubles approxi-mation augmented by a perturbative treatment of tripleexcitations [CCSD(T)]15 level) and applied to the evaluationof geometrical parameters, energies, as well as harmonic

Fig. 1 Geometry structures and atom labeling of the Ip and VIp conformers offree glycine.

a Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.

E-mail: vincenzo.barone@sns.it; Fax: +39 050 563513; Tel: +39 050 509134b Center for Nanotechnology Innovation @NEST, Istituto Italiano di Tecnologia,

Piazza San Silvestro 12, I-56127 Pisa, Italyc Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti

OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR,

Via G. Moruzzi 1, I-56124 Pisa, Italyd Dipartimento di Chimica ‘‘G. Ciamician’’, Universita di Bologna, Via Selmi 2,

I-40126 Bologna, Italy

† Electronic supplementary information (ESI) available: Methodology and com-putational details: (i) The best-estimated ab initio molecular structure; (ii) Thesemi-experimental equilibrium geometry; (iii) Best-estimated rotational andmolecular parameters; (iv) Best-estimated relative energies; (v) Best-estimatedharmonic frequencies and intensities; (vi) Anharmonic force-field and anharmo-nic corrections. Supplementary results: Best-estimated and DFT harmonic fre-quencies and IR intensities. See DOI: 10.1039/c2cp43884d

Received 1st November 2012,Accepted 29th November 2012

DOI: 10.1039/c2cp43884d

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frequencies and infrared (IR) intensities. More in detail, thecomposite schemes employed rely on extrapolation techniques(based on hierarchical basis set families) that allow us toaccount for truncation of basis sets and on the additivityapproximation to include core correlation.13,16–19 Anharmoniceffects are then introduced by means of density-functional-theory (DFT) computations employing the hybrid B3LYP func-tional in conjunction with purposely tailored basis sets.20–22

Second-order vibrational perturbation theory23–28 with properaccount of resonance effects,14,27,29–33 as well as effective hin-dered-rotor treatments,34 in conjunction with the so-calledsimple perturbation theory (SPT),14,35 have been employed. Tofurther validate our approach, the most stable glycine Ip con-former (see Fig. 1) has also been considered, as it has beenexperimentally very well characterized2–5,36 and thus the avail-able data can be used to benchmark our computations.

CCSD(T) calculations have been carried out with the quan-tum-chemical CFOUR program package,37 while DFT computa-tions have been performed employing the locally modifiedGAUSSIAN suite of programs for quantum chemistry.38 A fulland detailed account of the methodology employed is givenin the ESI.†

Molecular structures of the Ip and VIp conformers, asobtained by the composite procedure mentioned above, arecollected in Table 1, while the atom labeling is given in Fig. 1.On the basis of the literature on this topic (see, for example,ref. 11 and 39–42 and references therein), our computedmolecular structures are expected to have an accuracy of about

0.001 Å for bond lengths and 0.11 for angles. This is furtherconfirmed by the successful comparison, for the Ip conformer,of our computational results with the corresponding semi-experimental (SE) equilibrium structure, which is known tobe highly accurate.43 As described in the ESI,† the SE structurehas been derived from the experimental vibrational ground-state rotational constants and the corresponding computedvibrational corrections.44 The obtained SE is actually a partialmolecular geometry, which has been recently improved interms of the number of the determinable parameters as wellas their accuracy,10 and is further confirmed in this work byconsidering refined values for the fixed molecular parameters.The geometrical parameters of both conformers are quite closeto one another and do not show any significant trend, exceptfor the changes within the C1–O2–H4 frame related tothe trans–cis position of the H4 atom. In detail, we note thenarrowing of the O3–C1–O2 angle and the increase of theC5–C1–O2 and H4–O2–C1 angles. We can take advantage ofthe great accuracy of the structural data to provide the rota-tional parameters required to predict the rotational spectra,namely the vibrational ground-state rotational and quarticcentrifugal-distortion constants (see Table 2). Once again theagreement between experimental and computed data for the Ipconformer suggests relative errors smaller than 0.2% and 10%for the two sets of constants, which can be considered wellwithin the spectroscopic accuracy.‡ Nitrogen quadrupole-coupling constants are very similar for the Ip and VIp con-formers and therefore of no help for assignment purposes. Onthe other hand, the large dipole moment of VIp (especially its bcomponent) hints at a particularly intense rotational spectrumfor this conformer.

The high quality of the simulated IR spectra, which can beachieved for the Ip conformer, has been demonstratedrecently,10,31 showing also an improvement in accuracy of thehybrid approach over DFT results.31 Tables 3 and 4 report thebest-estimated harmonic frequencies and intensities of the VIp

Table 1 Molecular structures of the Ip and VIp conformers of glycine

Parameters

Ip/ttt VIp/ttc

Best rSEe

a Best

C1–O2 1.3476 1.34827(31) 1.3543C1–O3 1.2021 1.20331(62) 1.1961O3–C1–O2 123.05 122.991(31) 120.26O2–H4 0.9645 0.9645fix 0.9619H4–O2–C1 106.64 106.64fix 110.63C1–C5 1.5128 1.51318(47) 1.5227C5–C1–O2 111.35 111.482(41) 115.11C5–N6 1.4430 1.44245(14) 1.4407N6–C5–C1 115.25 115.285(17) 115.36C5–H7 1.0903 1.09078(7) 1.0926C5–H8 1.0903 1.09078(7) 1.0926H7–C5–C1 107.49 [107.36] 107.80H8–C5–C1 107.49 [107.36] 107.80H7–C5–C1–O3 �123.18 [�123.21] �122.62H8–C5–C1–O3 123.18 [123.21] 122.62N6–H9 1.0109 1.01044(10) 1.0111N6–H10 1.0109 1.01044(10) 1.0111H9–N6–C5 109.86 [110.10] 110.23H10–N6–C5 109.86 [110.10] 110.23H9–N6–C5–C1 57.93 [57.43] 58.35H10–N6–C5–C1 �57.93 [�57.43] �58.35H4–O2–C1–O3 0.0 0.0 180.0C5–C1–O3–O2 180.0 180.0 180.0N6–C5–C1–O3 0.0 0.0 0.0N6–C5–C1–O2 180.0 180.0 180.0H4–O2–C1–C5 180.0 180.0 0.0

a Semi-experimental equilibrium structure: this work. Values in squareparentheses have not been fitted directly. See text.

Table 2 Best-estimated rotational parameters of the Ip and VIp conformers ofglycine

Ip/ttt VIp/ttc

Main Deut Main Deut

Theo Expa

A0/MHz 10319.9 10341.521(89) 9918.5 10181.9 9395.6B0/MHz 3870.4 3876.1785(12) 3458.7 3879.2 3545.6C0/MHz 2908.4 2912.3509(10) 2679.1 2901.8 2689.1DJ/kHz 0.762 0.7434(33) 0.737 0.754 0.750DJK/kHz 4.184 3.986(17) 2.992 4.074 2.997DK/kHz 3.243 — 2.964 3.010 1.836d1/kHz �0.197 �0.190l(28) �0.157 �0.204 �0.184d2/kHz �0.014 �0.0158(17) 0.030 �0.027 0.007waa/MHz �1.278 — �1.057 �1.167 �0.745wbb/MHz �0.464 — �0.685 �0.524 �0.946wcc/MHz 1.742 — 1.742 1.691 1.691|wab|/MHz 3.830 — 3.847 3.867 3.879ma/D 0.809 — — �0.618 —mb/D �0.838 — — �2.953 —

a Ref. 2.

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conformer (for the main and tri-deuterated isotopologues,respectively), as obtained by means of the composite schemementioned above, along with their anharmonic counterpartswhich include the anharmonic terms at the DFT level (see ESI†for computational details, DFT harmonic results, and dissectedcontributions to best-estimated values). From a close inspec-tion of the ESI,† it is noted that on average DFT harmonicfrequencies agree well with the best-estimated values (within15 cm�1), thus confirming the reliability of DFT anharmoniccorrections. Anyway, in some cases inclusion of higher orderelectron-correlation effects (Do(T)) is required to ensureaccurate results; this is, for instance, the case of the best-estimated harmonic value for o4 (CH2 asymmetric stretch) ofthe VIp conformer, 3082 cm�1 (at the CCSD(T)/cc-pVTZ level),which should be compared with 3053 cm�1 and 3131 cm�1,computed at the B3LYP/SNSD and MP2/cc-pVTZ levels, respec-tively (the corresponding values for the Ip conformer are3107 cm�1, 3081 cm�1 and 3148 cm�1). The results at theanharmonic level can be directly compared with the experi-mental IR spectra recorded in low-temperature Ar, Kr and Xematrices.7 From the comparison of frequency values obtainedin different rare-gas low-temperature environments (bothmatrices and nanodroplets)3,6,7,36 and in the gas phase,4 itcan be noted that matrix effects are clearly observed for thehigher frequency modes (e.g.; red-shift of up to 25 cm�1 for OHstretching vibration) but are much less pronounced for theother observed transitions. For both the parent and deuteratedspecies, all the computed vibrational frequencies are in verygood agreement with their experimental counterparts, except

Table 3 Best-estimated harmonic and anharmonic frequencies (cm�1) and IRintensities (km mol�1) of the VIp conformer of glycine (main isotopologue)

Mode Sym.

Best estimates Exp.a

o Iharm n Ianh Ar Kr Xe

1 A0 3798 53.8 3611 44.5 3602.1w,3606.1w

3600.1vw 3576.8w

2 A00 3590 12.6 3416 9.43 A0 3514 5.6 3367 4.34 A00 3082 6.6 2937 9.55 A0 3036 24.3 2931 25.46 A0 1840 230.5 1803 100.2 1804.7s,

1807.7s1803.4s 1799.7m

7 A0 1676 20.0 1628 19.98 A0 1476 8.5 1436 7.79 A00 1403 0.0 1366 0.110 A0 1394 37.3 1378 33.111 A0 1298 332.7 1260 217.3 1256.6vs,

1259.3s1257.4vs 1256.3s

12 A00 1194 0.8 1166 0.413 A0 1176 11.0 1148 10.814 A0 1136 36.4 1108 42.1 1109w

(or 1101w)b1109.5w

15 A0 922 139.4 864 97.9 883.8mb 884.3m 881.3m16 A00 922 0.8 912 1.617 A0 837 33.3 814 52.7 808.1m18 A0 647 13.7 632 12.319 A00 568 9.6 547 5.720 A0 471 1.7 467 1.621 A00 466 84.4 439 88.722 A0 258 27.0 256 24.823 A00 195 57.4 193 53.924 A00 85 6.3 102 1.7

a Experimental results measured in low-temperature Ar, Kr and Xematrices, from ref. 7. b Uncertain assignment due to the nearby bandsof other conformers, see ref. 7.

Table 4 Best-estimated harmonic and anharmonic frequencies (cm�1) and IR intensities (km mol�1) of the VIp conformer of glycine ([ND2,OD] isotopologue)

Mode Sym.

Best estimates Exp.a

o Iharm n Ianh Ar Kr Xe

1 A0 3084 6.1 2937 8.6 2950.6w2 A00 3038 24.5 2933 28.8 2927.7w 2922.0w3 A0 2766 33.6 2670 29.3 2658.7s, 2661.6w, 2666.7w 2655.7s 2645.8s, 2640.0w4 A00 2647 8.4 2553 6.65 A0 2543 5.3 2477 4.66 A0 1833 245.6 1803 66.1 1804.3vs 1802.4s, 1798.9m 1795.5vs7 A0 1476 8.3 1436 5.68 A0 1400 10.3 1366 9.0 1343.7w 1340.0w9 A00 1329 0.1 1294 0.110 A0 1246 99.2 1218 72.411 A0 1223 212.6 1191 195.0 1196.3vs, 1193.4s 1198.2vs, 1194.5w 1199.3s, 1197.8sh12 A00 1105 39.7 1086 26.3 1084.8w 1081.7w 1080.5w13 A0 1085 1.2 1060 0.914 A0 950 1.0 928 0.715 A0 850 46.3 821 27.3 827.3m 827.5m 826.8m16 A00 796 1.6 789 2.017 A0 735 52.9 709 58.2 715.5m 712.9w 715.7m18 A0 610 15.6 597 16.9 604.4w 604.2w19 A00 543 0.6 538 0.720 A0 431 2.3 425 1.821 A00 361 48.7 339 46.422 A0 239 26.7 245 19.123 A00 152 29.3 160 32.024 A00 74 7.5 88 2.1

a Experimental results measured in low-temperature Ar, Kr and Xe matrices, from ref. 7.

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for n16 (A0, parent) and n8 (A0, [ND2,OD] isotopologue), whichshow discrepancies of about 20 cm�1. The first frequencycorresponds to a CC stretching + NH2 bending, and its assign-ment is uncertain due to the nearby bands of other confor-mers,7 whereas the second frequency refers to a CH2 in-planebending. However, the frequencies, used in ref. 7 for theunequivocal identification of the VIp conformer, namely, thefundamental O–H/D stretching,§ CQO stretching, and C–O–H/D bending/C–O stretching (see Fig. 2 for the correspondingspectral regions) are in very good agreement (in most cases wellbelow 10 cm�1) with the results from the MI-IR spectra.7

Moving to the low-frequency region, the characteristic frequen-cies of the n21 mode, corresponding to the out-of-plane O–H/Dbending (439 cm�1 and 339 cm�1, respectively), can be viewedas the VIp conformer ‘‘fingerprints’’ for possible Ramanexperiments.

The gas-phase thermodynamic properties of the VIp conformerof glycine, computed as differences with respect to the Ipconformer (i.e., conformational energies), are listed in Table 5.The temperatures of 15 K and 410 K have been selected, as they are

those employed in the recent IR6,7 and Raman4,5 experiments,respectively. In view of the lack of experimental estimates for thethermodynamic properties, the electronic energy difference(between the VIp and Ip conformers) has been computed bymeans of the same composite scheme16,17 used in the molecularstructure determination. We note that for energy differencesbetween rotational conformers, the post-CCSD(T) contributionswere found to be unimportant.45–47 Therefore, 1 kJ mol�1 for theerror resulting from our approach can be considered a reliableestimate. The corresponding vibrational contributions have beenincluded at both harmonic and anharmonic levels, as thoroughlydetailed in ref. 14. While computational studies of thermodynamicproperties for biomolecular building blocks can nowadays providea typical accuracy of about 10 kJ mol�1,48 our approach is expectedto provide an overall accuracy of about, or better than, 1 kJ mol�1

for conformational enthalpies.14 However, computations of accu-rate entropy contributions (1 J mol�1 K�1) to free energies offlexible molecules require the proper treatment of low-frequencytorsional motions and anharmonic effects.14 Table 5 shows that,due to the stiffness of the potential energy surface (PES) aroundthe VIp energy minimum, the harmonic approximation providesquite reasonable results, and also that temperature effects arequite limited. However, anharmonic effects are not negligible forthe other glycine conformers falling in flatter regions of thePES,4,5,10 so that only a full anharmonic-oscillator/hindered-rotorapproach can offer a reliable picture of the overall glycinebehavior.

In conclusion, state-of-the-art quantum-chemical computa-tions allowed us to complement the limited experimental datarecently reported for the elusive glycine VIp conformer, thusleading to a complete structural, thermodynamic, and spectro-scopic characterization with an accuracy rivaling the bestexperimental determinations for the most stable conformers.Together with the intrinsic interest of the results, the mostinteresting outcome of this and related work is, in our opinion,the promise that integrated experimental and computationalstudies can allow the characterization of medium-sizedmolecular systems of biological and/or technological interest

Fig. 2 Computed IR spectra of the Ip and VIp conformers of glycine (main isotopologue). In the three panels the regions of MI-IR spectra corresponding to the O–Hstretching, CQO stretching, and C–O–H bending/C–O stretching, selected in ref. 7 to demonstrate the formation of the VIp conformer upon NIR laser irradiation, areshown.

Table 5 Theoretical thermodynamic propertiesa of the VIp conformer of glycineat low and high temperature

HO HO + HRb SPT (HRAO)b,c

DEele [kJ mol�1] 20.32DEZPVE [kJ mol�1] 19.89 19.80

T = 15 KDH [kJ mol�1] 19.89 19.80 19.81DG [kJ mol�1] 19.89 19.77 19.80

T = 410 KDH [kJ mol�1] 20.07 20.08 20.24DG [kJ mol�1] 20.34 20.24 20.26

a Conformational energies. All thermodynamic properties have beencomputed at 1 atm. b The two lowest vibrations have been described byhindered-rotor contributions computed by means of an automaticprocedure.34 c Contributions computed by means of the HDCPT214

model using the hybrid CC/DFT force field, in conjunction with simpleperturbation theory (SPT)14,35 (see text for details).

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with an accuracy reached so far only for very small rigidmolecules.

Acknowledgements

This work was supported by Italian MIUR (PRIN 2009 and FIRBfunds). The high performance computer facilities of theDREAMS center (http://dreamshpc.sns.it) are acknowledgedfor providing computer resources. The support of theCOST-CMTS Action CM1002 ‘‘COnvergent Distributed Environ-ment for Computational Spectroscopy (CODECS)’’ is alsoacknowledged.

References‡ While for vibrational spectroscopy there is a general agreement that‘‘spectroscopic accuracy’’ refers to vibrational frequencies accurate towithin �1 cm�1, for rotational spectroscopy this limit has never beenclearly defined. For rotational constants, the ‘‘spectroscopic accuracy’’can be reasonably set at 10 MHz.§ Considering a plausible matrix effect, a red-shift of about 20 cm�1,an unperturbed O–H stretching frequency can be estimated as3620 cm�1.

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