Molecular Structure and Spectroscopic Parameters of the Thiouracil

Article pubs.acs.org/JPCA

Microsolvation of 2‑Thiouracil: Molecular Structure and Spectroscopic Parameters of the Thiouracil−Water Complex Cristina Puzzarini*,† and Malgorzata Biczysko‡,§ †

Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via Selmi 2, I-40126 Bologna, Italy Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy § Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR, Consiglio Nazionale delle Ricerche, Via G. Moruzzi 1, I-56124 Pisa, Italy ‡

S Supporting Information *

ABSTRACT: State-of-the-art quantum-chemical computations have been employed to accurately determine the equilibrium structure and interaction energy of the 2-thiouracil−water complex, thus extending available reference data for biomolecule solvation patterns. The coupled-cluster level of theory in conjunction with a triple-ζ basis set has been considered together with extrapolation to the basis set limit, performed by employing second-order Møller−Plesset perturbation theory, and inclusion of core-correlation and diffuse-function corrections. On the basis of the comparison of experiment and theory for 2-thiouracil [Puzzarini et al. Phys. Chem. Chem. Phys. 2013, 15, 16965−16975], structural changes due to water complexation have been pointed out. Molecular and spectroscopic properties of the 2-thiouracil−water complex have then been studied by means of the composite computational approach introduced for the molecular structure evaluation. Among the results achieved, we mention the accurate determination of the molecular dipole moment and of the spectroscopic parameters required for predicting the rotational spectrum.

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INTRODUCTION

In recent years, one of the most powerful approaches to derive the structure of flexible molecules and molecular complexes has been the analysis of the corresponding vibrationally resolved spectra.4,18 However, ambiguities in their interpretation might lead to erroneous conclusions, as demonstrated for instance by the anisole−water adduct.13 For the latter, experimental resonance enhanced multiphoton ionization (REMPI) and IR-REMPI double resonance measurements combined with calculations at the MP2 level19 predicted a nonplanar equilibrium structure. This assumption was subsequently corrected on the basis of the analysis of the ground-state rotational constants, thus pointing out that water is located in the anisole symmetry plane.2,12,20 This example points out the need of reference data for studies of intermolecular interactions, also including microsolvation. Among the various spectroscopic techniques, rotational spectroscopy is the most suited for these purposes because of its inherent high resolution and its ability to infer structural information.21−23 Rotational spectroscopy is a powerful technique whose applicability to the investigation of biomolecular systems in the gas phase has recently been further

In the past decade, many gas-phase spectroscopic investigations have focused on the understanding of the nature of weak interactions in model biological systems, and a great effort has been devoted to studies dealing with complexes formed by small biomolecules with either water or other solvents (see, for example, refs 1−17 and references therein). A number of different issues relevant to understand the properties of bulk or solvated systems can be addressed from experimental investigations on molecular complexes. In the gas phase, the focus is on interactions between the molecules considered, as the case of DNA bases pairing (e.g., ring stacking), and with solvent molecules (e.g., hydrogen bond). With respect to the latter case, hydrogen bond cooperativity has been identified to be one of the most important factors that contribute to the stabilization of hydrated biomolecules. Because the hydration of the nucleic acids controls their structure and mechanism of action, the study of the interactions of water with the individual nuclear bases constitutes the first step toward the understanding of the effects of hydration on DNA. The study of the molecular properties of hydrated systems containing a limited number of water molecules (microsolvation) is the basis for understanding the solvation process and how structure and reactivity vary from isolation to solution. The aim is to understand the role played by the forces involved at a molecular level. © XXXX American Chemical Society

Special Issue: Jacopo Tomasi Festschrift Received: October 19, 2014 Revised: November 28, 2014

A

dx.doi.org/10.1021/jp510511d | J. Phys. Chem. A XXXX, XXX, XXX−XXX

The Journal of Physical Chemistry A

Article

Figure 1. Structures and relative energies of the four most stable 2-thiouracil−water complexes.

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METHODOLOGY Geometry optimizations as well as equilibrium energy and molecular property evaluations were carried out at the coupledcluster (CC) level of theory employing the CC singles and doubles approximation augmented by a perturbative treatment of triple excitations (CCSD(T)),42 and using second-order Møller−Plesset perturbation theory (MP2).43 Both methods were used in conjunction with the correlation-consistent, (aug)cc-p(C)VnZ (n = T, Q), basis sets.44−47 MP2 and CCSD(T) geometry optimizations were performed with the quantumchemical CFOUR program package48 using analytic derivative techniques.49 Density functional theory (DFT) was used to compute harmonic and anharmonic force fields. Within the DFT approach, the hybrid B3LYP50 and double-hybrid B2PLYP51−53 functionals were considered in conjunction with the SNSD54,55 and aug-cc-pVTZ basis sets, respectively. DFT computations were carried out employing the Gaussian suite of programs for quantum chemistry.56 To study the microsolvation of 2-thiouracil through rotational spectroscopy and related properties, the following determinations are required: (a) Molecular structure. Equilibrium structure is actually the main property of interest. Because rotational constants are inversely proportional to the moments of inertia, which in turn are related to the molecular structure, the evaluation of the equilibrium geometry permits one to infer information on rotational spectroscopy and viceversa. (b) Rotational parameters. They include rotational and centrifugal-distortion constants. The former are the leading terms for this spectroscopic technique and the determination of their equilibrium values mainly involve geometry optimizations. To derive the parameters actually obtainable from the spectral analysis, i.e., the vibrational ground-state rotational constants, the computation of the corresponding vibrational corrections is required. As concerns centrifugal distortion, this effect arises from the fact that bond distances and angles vary not only because of molecular vibration but also because of the centrifugal force produced by rotation. Both centrifugaldistortion terms and vibrational corrections to rotational constants require force-field calculations. (c) Hyperf ine parameters. Hyperfine parameters describe the hyperfine interactions involving nuclear spins that lead to the so-called hyperfine structures in the rotational spectrum. Among the various hyperfine parameters, those of interest in this context are the nuclear quadrupole-coupling constants because they are strongly connected to the mass distribution and intramolecular interactions. (d) Energetics. Energy evaluations provide information on the stability of the complex and on the population of different isomers. To gain physical significance, the equilibrium energy

improved by the introduction of laser ablation vaporization sources, thus permitting one to overcome the problems of thermal decomposition associated with conventional heating methods (see for example ref 24 and references therein), and by the employment of chirped-pulse excitation, which allows for broadband measurements, thus reducing measurement time and sample consumption.25 Furthermore, quantum-chemical computations have nowadays reached such an advanced level that highly accurate results can be achieved for energies and properties of small to medium-sized molecules, which can rival experiments (see, for instance, refs 22 and 26−28 and references therein) and can be employed for benchmarking purposes. In fact, they allow one to estimate the accuracy of computationally inexpensive quantum-chemical approaches applicable to larger biomolecular systems,29−36 which in turn can be used for conformational analysis and modeling of biomolecules37,38 in solution. The subject of the present investigation is the complex formed by 2-thiouracil, the most stable isomer of thiouracil, and one molecule of water. Thiouracil and its derivatives are of particular interest for their presence as minor components in natural t-RNAs39 and their thyroid-regulating activities,40 and they represent an example of biosystem including the thiocarbonyl (−C(S)−) bond pattern. As pointed out in ref 41, some thiouracil derivatives are used both as drugs for increasing the hypothyroidism effect on blood and as important components of dietary products; in particular, 2-thiouracil is important for its anticancer and antiviral activity, related to its ready incorporation into nucleic acids (see ref 41 and references therein). The natural continuation of the study carried out in ref 41 is therefore the structural and spectroscopic characterization of the thiouracil−water complex. To this end, in this manuscript we report a high-level quantumchemical investigation of its equilibrium structure, and molecular and spectroscopic properties. In addition to provide the first accurate characterization of the thiouracil−water complex, this work also summarizes all information required to experimentally study this complex by means of rotational spectroscopy. Such an experimental investigation would permit the confirmation of the molecular structure and properties here derived. This manuscript is organized as follows. In the next section, the methodology and computational details are introduced and detailed by describing the theoretical and computational requirements for structural, spectroscopic, and energetic determinations. Thereafter, the results are presented and discussed. B



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difference needs to be corrected by including vibrational contributions. For 2-thiouracil, the spectroscopic and molecular parameters from ref 41 are mostly used. When required, they were also determined in the frame of the present study. To characterize the lowest-energy complexes, a preliminary investigation of the potential energy surface was carried at the B3LYP/SNSD level, with the electronic energies estimated at the B2PLYP/aug-cc-pVTZ level. Figure 1 depicts the optimized equilibrium structures of the four thiouracil−water complexes considered, along with their anharmonic zero-point corrected energies (with corrections computed at the B3LYP/SNSD level). Analogously to uracil,9,57 the conformer denoted as W1 was found to be the most stable with a population of about 90%. Therefore, it is the only one considered in the following. Molecular Structure. To accurately determine the molecular structure of the W1 2-thiouracil−water complex, a composite approach was employed. This mainly involves MP2 geometry optimizations, with the CCSD(T) method used to include the effects of triple excitations. Though a detailed description of this composite scheme can be found for example in refs 41, 58, and 59, we briefly note that within this approach all contributions and corrections are considered directly on the geometrical parameters. To emphasize that this approach is mainly based on MP2 calculations, instead of the more expensive CCSD(T) ones,60 it has been denoted as a “cheap” composite scheme,61 where the word “cheap” is used to stress the reduced computational cost. Within this scheme, to account for basis-set truncation effects, the complete basis set (CBS) limit was evaluated by making use of the n−3 extrapolation form62 applied to the case n = T and Q: 3

r(CBS) =

B0β = Beβ + ΔBvib = Beβ −

1 Ĥ = 2 −

(3)

i

∑ (Jβ̂

− πβ̂ )μβγ (Jγ̂ − πγ̂ ) +

β ,γ

1 8

1 2

∑ ωipi 2̂

+ V (q)

i

∑ μββ (4)

β

which is expressed in dimensionless normal coordinates qi, with ωi being the associated harmonic frequency (in cm−1) and p̂i the conjugated momentum. Jβ̂ is the rotational angular momentum operator about the inertial axis β, and π̂β represents the βth component of vibrational angular momentum. μβγ denotes the elements of an effective reciprocal inertia tensor. The final term in the Hamiltonian above is usually denoted as the Watson term and is necessitated by the choice of the normal coordinate representation. Finally, V(q) is the potential energy surface, which is expanded as a Taylor series in qi: V (q) =

1 2

∑ ωiqi 2 +

+

1 24

i

1 6

∑ ϕijkqiqjqk ijk

∑ ϕijklqiqjqkql + ... ijkl

(5)

where ϕijk and ϕijkl are the cubic and quartic force constants, respectively. For our purposes, this series is truncated after the second term. Within Rayleigh−Schrö dinger perturbation theory, the Watson Hamiltonian is partitioned into the rigid-rotor harmonic-oscillator Hamiltonian, Ĥ 0, and a perturbation Ĥ ′:

(1)

with n = 4, and r(n) and r(n − 1) thus denoting the MP2/ccpVQZ and MP2/cc-pVTZ optimized parameters, respectively. Even though this procedure is only empirically based, the investigation of ref 63 demonstrated its reliability and accuracy. The effects due to core−valence (CV) electron correlation were included by means of the corresponding correction, Δr(CV), derived as the difference between the geometries optimized at the MP2/cc-pCVTZ level correlating all and valence electrons only. Similarly, the correction related to the effect of diffuse functions, Δr(diff), was evaluated by the difference between the geometries optimized at the MP2 level in conjunction with the aug-cc-pVTZ and cc-pVTZ basis sets, within the frozen-core approximation. The higher-order correlation energy contributions were included via the Δr(T) correction derived from the comparison of the geometries optimized at the MP2 and CCSD(T) levels (both with the ccpVTZ basis set). On the whole, our best-estimated equilibrium structure was determined as r(best) = r(CBS) + Δr(CV) + Δr(diff) + Δr(T)

∑ αi β

where αβi ’s are the vibration−rotation interaction constants, with i and β denoting the normal mode and the inertial axis, respectively. These constants were obtained by means of vibrational second-order perturbation theory (VPT2).64 The starting point of VPT2 is the semirigid Watson Hamiltonian:65

3

n r(n) − (n − 1) r(n − 1) n3 − (n − 1)3

1 2

0 Ĥ = Ĥ + Ĥ ′

ℏ2 0 Ĥ = 2

(6) 2

Jβ̂

∑

I βe

β

+

1 2

∑ ωi(pi 2 + qi 2) i

(7)

where ℏ defines the equilibrium rotational constant Bβe . Although there are no first-order corrections to Bβe , in second order the usual contact transformation method gives the following result64 2

/2Ieβ

Biβ = Beβ −

⎛

∑ αi β⎝vi + ⎜

i

1 ⎞⎟ 2⎠

(8)

which leads to eq 3 once all vi are equal to zero. It is important to point out that the individual αβi constants might be subject to resonances, but their sum (corresponding to the ΔBvib correction of eq 3) is unaffected. In the present study, the required cubic force field was obtained at the B3LYP/SNSD level. For a given vibrational state, the phenomenological rotational Hamiltonian, Ĥ rot, up to sixth degree in the components of the rotational angular momentum can be written as21

(2)

In both eqs 1 and 2, r is a generic structural parameter, thus denoting either a bond distance or an angle. Rotational and Hyperfine Parameters. Equilibrium rotational constants, Bβe , were straightforwardly derived from the best-estimated equilibrium structure obtained as described in the previous section. By correcting them for vibrational effects,64 we derived the vibrational ground-state constants, Bβ0: C



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Table 1. Equilibrium Structure (Distances in Å, Angles in deg) and Binding Energy (kJ mol−1) of the W1 2-Thiouracil−Water Complex 2-thiouracil−water B3LYP/SNSD N1−C2 C2−N3 N3−C4 C4−C5 C5−C6 C6−N1 C2−S7 C4−O8 N1−H9 N3−H10 C5−H11 C6−H12 N1−O13 O13−H9 O13−H14 O13−H15 S7−O13 S7−H14

1.3678 1.3656 1.4173 1.4534 1.3518 1.3727 1.6859 1.2179 1.0283 1.0150 1.0814 1.0849 2.8332 1.8472 0.9799 0.9648 3.2434 2.4015

C2−N1−C6 C5−C4−N3 C4−N3−C2 N3−C2−N1 N3−C2−S7 N3−C4−O8 C2−N1−H9 C2−N3−H10 C6−C5−H11 N1−C6−H12 O13−N1−C2 O13−H9−N1 H14−O13−N1 H15−O13−N1 H15−O13−N1−C2

122.95 113.30 127.66 114.43 122.31 119.80 116.45 116.48 122.10 114.86 103.41 159.46 78.05 129.22 −101.38

Ae Be Ce

2401.49 870.10 639.54

ΔEb ΔECPc ΔECP+ZPVd

−46.6 −45.0 −36.8e

B2PLYP/aug-cc-pVTZ

2-thiouracil

CCSD(T)/cc-pVTZ

Distances 1.3636 1.3627 1.4122 1.4490 1.3479 1.3689 1.6730 1.2166 1.0221 1.0106 1.0762 1.0794 2.8221 1.8411 0.9749 0.9612 3.2389 2.4042 Angles 122.98 113.20 127.86 114.26 122.35 119.90 116.39 116.31 121.96 114.96 103.53 159.72 78.19 130.85 −101.97 Rotational Constants 2416.40 876.04 643.74 Energies −43.0 −41.2 −32.3f

best “cheap”a

1.3627 1.3658 1.4124 1.4578 1.3513 1.3761 1.6765 1.2153 1.0229 1.0111 1.0782 1.0815 2.8027 1.8182 0.9728 90.608 3.2359 2.3962

1.3636 1.3611 1.4028 1.4489 1.3457 1.3707 1.66441 1.2133 1.0175 1.0099 1.0770 1.0798 2.8444 1.8398 0.9711 0.9583 3.2382 2.4034

best “cheap”a 1.3654 1.3631 1.4017 1.4522 1.3448 1.3714 1.6496 1.2130 1.0058 1.0098 1.0768 1.0796

122.83 113.05 127.99 114.49 122.03 120.18 116.33 116.02 122.00 114.92 103.72 160.34 77.76 122.77 −99.41

122.97 113.20 127.86 114.26 122.04 119.91 116.37 116.32 122.20 114.98 103.21 160.04 77.94 133.54 −100.56

123.69 113.84 127.78 113.78 123.69 119.99 115.18 116.06 122.19 115.29

2403.91 878.48 644.37

2437.58 875.86 645.08

3578.60 1322.36 965.56

−50.95 −42.77 −33.90f

−41.06 −41.06 −32.19f

Best-estimated equilibrium structure obtained by means of the “cheap” scheme (eq 2). bInteraction energy. cCounterpoise-corrected interaction energy according to eq 13. dZPV-corrected interaction energy according to eq 14. eZPV correction (−8.2 kJ mol−1) computed at the B3LYP/SNSD level. fZPV correction (−8.87 kJ mol−1) computed at the hybrid B2PLYP/AVTZ//B3LYP/SNSD level. a

1 Ĥ rot = 2 +

∑ μαβ Jα̂ Jβ̂ α ,β

∑ α ,β ,γ ,δ ,ε,η

+

1 4

∑

ταβγδJα̂ Jβ̂ Jγ̂ Jδ̂

ταβγδ = −

α ,β ,γ ,δ

ταβγδεηJα̂ Jβ̂ Jγ̂ Jδ̂ Jε̂ Jη̂ + ...

1 2

∑ μαβi (ωr)−1μγδi i

(10)

with μiαβ being the first derivative of μαβ with respect to the ith normal coordinate. The empirical determinable coefficients are actually Watson’s reduction quartic centrifugal-distortion constants.65 Their relations to ταβγδ’s can be found for instance in ref 65. In the present case, the symmetric-top reduction (Watson’s S reduction) is considered.66 To evaluate the quartic centrifugal-distortion constants, in this study a harmonic force field at the B2PLYP/aug-cc-pVTZ level was used.

(9)

where the summations run over the inertial axes. The second and third terms are those that introduce contributions due to centrifugal distortion, with ταβγδ and ταβγδεη being the effective quartic and sextic centrifugal-distortion constants, respectively. The former are given by the expression D



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⎡

The components of the molecular electric dipole moment and of the electric field gradient tensors at the nitrogen nuclei were computed at the equilibrium by means of a composite scheme analogous to that employed for the molecular structure determination. The corresponding vibrational corrections were evaluated at the B3LYP/SNSD level by performing a vibrational averaging of the molecular property P by means of VPT2,67 using anharmonic vibrational wave functions, as implemented in Gaussian:56 ΔP = −

+

ℏ 4

∑

ℏ 4

∑

i

i

1 ⎛⎜ ∂P ⎞⎟ ⎜ ⎟ ωi 2 ⎝ ∂qi ⎠

∑ 0

j

ϕijj ωj

coth

Z kinetic = 16 ∑ β

(11)

TW TW = E TW − E TTW − E W

(15)

Figure 2. Molecular structure and atom labeling of the W1 2thiouracil−water complex.

Supporting Information, it is evident that the corrections due to the extrapolation to the CBS limit, with respect to the MP2/ccpVQZ level of theory, range from less than 0.001 Å for the C− H and O−H bonds to ∼0.003 Å for larger distances; for angles, in all cases but the H15−O13−N1 angle, the corrections are smaller than 0.1°, whereas for the latter the correction is about 2°. The effects of core correlation shorten all bond distances, with corrections ranging from less than 0.001 to about 0.003 Å, where the smallest contributions are again observed for the C− H and O−H bonds. Because triple excitations are known to play a relevant role in accurate molecular structure evaluations,22,76−78 large effects are usually observed. In the present case, it is rather surprising that the corrections to bond lengths are on the same order as CV corrections, but either positive or negative. For angles, the effects of core correlation turn out to be smaller than those due to triple excitations, with the latter ranging from 0.1 to 0.3°. The inclusion of diffuse functions provides the smallest corrections, except for the structural parameters describing the interaction between thiouracil and the water molecule, in line with the fact that inclusion of diffuse functions is required for correctly describing noncovalent interactions.13 Despite the present study being the first application of the so-called “cheap” composite scheme61 to a hydrogen-bonded complex, the analysis of the various

(13)

where EYX is the energy of the subsystem X computed with the Y basis set; TW, T, and W denote the complex, thioracil and water, respectively. Subsequently, the interaction energies were corrected for the anharmonic zero-point vibrational (ZPV) contribution computed at the B3LYP/SNSD level. The following resonance-free formulation in the VPT2 treatment74,75 was employed:

+

⎥⎦

(12)

TW W TW W ΔECP = [E TW − E TT − E W ] − [E TTW − E TT] − [E W − EW ]

E0 = E0

j>i

RESULTS AND DISCUSSION Molecular structure. The equilibrium structures of the 2thiouracil−water as obtained at the MP2 level using the tripleand quadruple-ζ basis sets, the extrapolated CBS structure (eq 1) as well as the equilibrium geometries resulting from the inclusion of the various corrections together with the bestestimated equilibrium structure (eq 2) are collected in the Supporting Information. In Table 1, the best-estimated results together with those at the CCSD(T)/cc-pVTZ, B2PLYP/augcc-pVTZ and B3LYP/SNSD levels are reported. For atom labeling, the reader is referred to Figure 2. From the table in the

where eQ in the present case is the nitrogen quadrupole moment, 0.02044(3) barn, taken from ref 71. On the other hand, the dipole moment components allow one to predict what type of rotational transitions can be observed and their intensities.21 Energetics. For the determination of the complex stabilization energy, a composite scheme similar to that used for the molecular structure determination was employed, with the basis-set superposition error (BSSE) also considered. In the case of CBS energies, by definition, the BSSE vanishes.72 The best-estimated binding energy was thus evaluated as the electronic energy difference between the thiouracil−water complex and the sum of the energy of isolated monomers (first term within squared brackets of eq 13). In all other cases, the BSSE was taken into account via counterpoise correction (CP):73

(0)

i

■

where kB is the Boltzmann constant and T denotes the temperature. A detailed account can be found in refs 68−70. Note that on the one hand, the computation of the electric field gradient tensors, qαβ, permits one to straightforwardly derive the nuclear quadrupole-coupling constants χαβ: χαβ = eQqαβ

∑∑

with denoting the Coriolis constant coupling the ith and jth normal modes along the inertial axis β. The best-estimated, hybrid B2PLYP/B3LYP ZPV was then obtained by replacing in eq 14 the E0(0) computed at the B2PLYP/aug-cc-pVTZ level.

2kBT

0

⎣

⎤

(ζijβ)2 ⎥

ζβij

ℏωj

⎛ ⎞ ℏωi 1 ⎜ ∂ 2P ⎟ coth ⎜ 2⎟ ωi ⎝ ∂qi ⎠ 2kBT

e ⎢ μββ ⎢

⎧ϕ ⎪ iijj + ∑∑⎨ − ⎪ i j ⎩ 32

⎡ϕ ϕ iik jjk

∑ ⎢⎢ k

⎣ 32ωk

⎤⎫ ⎪ ⎥⎬ + Z kinetic 48(ωi + ωj + ωk) ⎥⎦⎪ ⎭ ϕijk 2

(14)

where E0(0) is the harmonic ZPV energy, and E



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Table 2. Spectroscopic Parametersa of the W1 Thiouracil− Water Complex and Thiouracil

contributions performed above pointed out the typical behavior already observed for semirigid molecules41,58,60 as well as for a flexible system.79 Therefore, on the basis of the available literature (see, for example, refs 41, 58, 60, and 79), conservative estimates for the resulting best-estimated geometrical parameters are 0.002 Å for bond lengths and 0.1° for angles. Concerning the performance of the DFT models considered, it should be noted that for bond distances the B3LYP/SNSD level of theory shows the usual overestimation (see, for example, ref 60), whereas an extremely good agreement of the B2PLYP/aug-cc-pVTZ parameters with the best-estimated ones is observed. This finding is encouraging in relation to the study of building blocks of biomolecules because of the low computational cost of the B2PLYP/aug-cc-pVTZ level compared to the cost of the composite approach. For comparison purposes, in Table 1 the best-estimated equilibrium structure of 2-thiouracil, obtained in ref 41 with the same composite approach, is reported. From such a comparison, we note that most of the structural parameters of 2-thiouracil are little affected by the complexation with a water molecule; i.e., for bond distances the differences are of the order 0.001−0.002 Å. Only those parameters directly involved in the hydrogen bonds vary significantly upon complexation. For instance, the N1−H9 distance enlarges from 1.0058 to 1.0175 Å when going from 2-thiouracil to the W1 complex. The C2−S7 bond length increases from 1.6496 to 1.6644 Å, as a consequence of the fact that the S atom acts as a hydrogen-bond acceptor. In Table 1, the binding energies of the complex are also compared. As already noted for equilibrium geometry, a very good agreement is obtained between the best-estimated value and the counterpoise-corrected value at the B2PLYP/aug-ccpVTZ level, the discrepancy being on the order of 0.3%. On the other hand, the CCSD(T)/cc-pVTZ overestimates the best value by about 4%, whereas even larger (∼10%) is the overestimation observed at the B3LYP/SNSD level of theory. The last comment concerns the reliability of our composite approach. First of all, it should be noted that composite schemes have been largely used for validating less expensive computational methodologies in the evaluation of interaction energies for hydrogen-bonded and stacked dimers of nucleobases (the reader is for instance referred to refs 80−83). In particular, our approach was proved to provide accurate and reliable results for the conformational energy of a flexible molecule like the glycine-dipeptide analogue investigated in ref 79. Rotational Spectrum. In Table 1, the equilibrium rotational constants as straightforwardly derived from the corresponding equilibrium structures are also reported. Those of interest are the best-estimated equilibrium rotational constants, that is, those corresponding to the best-estimated equilibrium structure. These equilibrium rotational constants have been augmented by vibrational corrections at the B3LYP/ SNS level, according to eq 3, to determine our best estimates for the vibrational ground-state rotational constants. The values obtained are reported in Table 2 together with the best estimates for the nitrogen quadrupole-coupling constants and the quartic centrifugal-distortion constants at the B2PLYP/augcc-pVTZ level. The corresponding parameters for 2-thiouracil, evaluated at the same level of theory (ref 41 and this work), are also collected in Table 2.

2-thiouracil− water

2-thiouracil

parameter

calculatedb

experimentb,c

calculatedb

A0/MHz B0/MHz C0/MHz DJ/kHz DJK/ kHz DK/kHz d1/kHz d2/kHz

2421.763 868.164 639.803 0.0330 0.0709 0.7475 −0.0099 −0.0017

3555.18805(64) 1314.86002(27) 960.03086(16)

3555.458 1315.287 960.200 0.0315(0.0319)d 0.0548(0.0564)d 0.5820(0.5912)d 0.0112(−0.0114)d −0.0022(−0.0022)d

χaa/MHz χbb/MHz χcc/MHz χab/MHz χac/MHz χbc/MHz χaa/MHz χbb/MHz χcc/MHz χab/MHz χac/MHz χbc/MHz μa/D μb/D μc/D

0.804 2.021 −2.825 −0.596 0.001 −0.029 1.846 1.144 −2.990 0.119 −0.032 −0.019 2.16 −3.72 −1.31

N1e 1.634(10) 1.777(12) −3.411(12)

N3e 1.726(10) 1.399(13) −3.125(13)

1.577 1.783 −3.360 0.280

1.728 1.344 −3.072 −0.333

0.63 4.62

a

Watson S-reduction. bBest-estimated equilibrium rotational (from best-estimated equilibrium structure) and nitrogen quadrupolecoupling constants, and dipole moment components augmented by vibrational corrections at the B3LYP/SNSD level. Quartic-centrifugal distortion constants at the B2PLYP/aug-cc-pVTZ level. See text. c Reference 41. dIn parentheses the best-estimated quartic centrifugaldistortion constants are given.41 eFor atom labeling, see Figure 2.

The spectroscopic parameters of Table 2 can be used to simulate the rotational spectra of both systems. An example is provided by Figure 3, which depicts the comparison of the two rotational spectra in the 4−12 GHz frequency range. The predicted spectra do not account for the nitrogen quadrupole coupling, i.e., the corresponding hyperfine structure is not displayed. The reason at the basis of this choice is that preliminary investigations are usually carried out using a chirped pulse Fourier transform microwave (CP-FTMW) spectrometer (with a laser ablation source), which does not permit one to resolve the hyperfine structure. The reader is for instance referred to ref 41. From Figure 3, it is evident that the rotational spectrum of the complex is sufficiently strong to be detected, even taking into account a limited formation of the complex in the gas phase. In Table 2, the experimental results for 2-thiouracil are also given. Their comparison to the corresponding computed spectroscopic parameters allows us to derive the expected accuracy for the computed constants of the complex. We note that for rotational constants the agreement is very good, with discrepancies in the range 0.01−0.03%, whereas for nuclear quadrupole-coupling constants the differences increase to, on average, 2%. Therefore, we expect that the computed rotational and nitrogen quadrupole-coupling constants of the complex are conservatively affected by an uncertainty of 0.1% and 3%, F



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Figure 3. Computed rotational spectra of the W1 2-thiouracil−water complex (in red) and 2-thiouracil (in blue) in the 4−12 GHz frequency range. The experimental stick spectrum of 2-thiouracil is also shown (in black, dashed line). In the inset on the left the 7−8 GHz range is highlighted, with the comparison of experiment and theory for the J = 40,4 ← 31,3 of 2-thiouracil better shown in the right-hand side inset.

information derivable from the rotational constants. In fact, as mentioned in the Methodology section, they are inversely proportional to the moments of inertia, which in turn are related to the molecular structure. By applying the so-called semiexperimental approach,84 we can determine equilibrium geometrical parameters of experimental quality.22,23,85 This approach is based on experimental ground-state rotational constants computationally corrected for vibrational effects, with the corresponding corrections obtained from cubic-force-field calculations. For a detailed account on this approach, the reader is referred, for example, to refs 22, 23, 78, and 85. In view of what pointed out above, only rotational and quartic centrifugaldistortion constants are reported in Table 3. We note that the differences in these parameters, when moving from one isotopic species to another, are such that completely different rotational spectra are derived. As pointed out above, in view of the relationship between molecular structure and rotational constants, the latter can be used not only for structural determinations but also for the unequivocal identification of the conformers present in the gasphase mixture investigated. In addition to rotational constants, nuclear quadrupole-coupling constants can also be used to infer structural information. In fact, rotational constants provide information on the mass distribution, whereas quadrupolecoupling constants yield information on the electronic environment of the quadrupolar nuclei and can be decisive to identify conformers with similar mass distributions but different intramolecular interactions. In the present case, from Table 2 we note that, when moving from 2-thiouracil to the complex, the largest changes are observed for the nuclear quadrupolecoupling constants of N1, which is indirectly involved in the complex formation (whereas N3 is not involved at all). For example, χaa(N1) varies by about 50%, whereas χaa(N3) changes by about 7% only. We furthermore note that for both nitrogens the χac and χbc off-diagonal terms are very close to zero, thus meaning that the ring structure of 2-thiouracil is very close to planarity also in the complex.

respectively. For quartic centrifugal-distortion constants, the lack of experimental data prevents an accurate estimation of the errors affecting the B2PLYP/aug-cc-pVTZ parameters. On the other hand, for 2-thiouracil the best-estimated values are also available (given in parentheses in Table 2). From the literature on this topic,58,60 the accuracy of the latter is estimated to be in relative terms about 1%. Because for 2-thiouracil the B2PLYP/ aug-cc-pVTZ quartics are underestimated by about 2% with respect to the best-estimated values, the corresponding constants of the complex are conservatively expected to be affected by uncertainties of the order of 3%. Finally, in Table 3 the computed results (at the same level as those given in Table 2) for the 34S-thiouracil−water, Table 3. Computed Spectroscopic Parametersa,b of Isotopic Species of the W1 Thiouracil−Water Complex parameter A0/MHz B0/MHz C0/MHz DJ/kHz DJK/ kHz DK/kHz d1/kHz d2/kHz

34

S-thiouracil−water 2371.722 860.525 632.143 0.0316 0.0698 0.7507 −0.0095 −0.0016

thiouracil−D2O 2392.111 830.375 617.670 0.0316 0.0801 0.7785 −0.0091 −0.0015

34

S-thiouracil−D2O 2340.514 824.043 610.703 0.0306 0.0754 0.7664 −0.0089 −0.0015

a

Watson S-reduction. bBest-estimated equilibrium rotational (from best-estimated equilibrium structure) constants augmented by vibrational corrections at the B3LYP/SNSD level. Quartic-centrifugal distortion constants at the B2PLYP/aug-cc-pVTZ level. See text.

thiouracil−D2O and 34S-thiouracil−D2O isotopic species are collected. These isotopologues have been chosen because of the nonzero chances of observing the corresponding rotational spectra: the natural abundance of 34S is about 5%, and heavy water is easily available. The interest in isotopic species, and in particular, on those with isotopic substitution on atoms involved in hydrogen bonds is related to the structural G



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(3) de Vries, M. S.; Hobza, P. Gas-phase spectroscopy of biomolecular building blocks. Annu. Rev. Phys. Chem. 2007, 58, 585−612. (4) Reha, D.; Valdes, H.; Vondrasek, J.; Hobza, P.; Abu-Riziq, A.; Crews, B.; de Vries, M. S. Structure and IR spectrum of phenylalanylglycyl-glycine tripetide in the gas-phase: IR/UV experiments, ab initio quantum chemical calculations, and molecular dynamic simulations. Chem.Eur. J. 2005, 11, 6803−6817. (5) Alonso, J.; Cocinero, E.; Lesarri, A.; Sanz, M.; Lopez, J. The glycine-water complex. Angew. Chem., Int. Ed. 2006, 45, 3471−3474. (6) Blanco, S.; Sanz, M. E.; López, J. C.; Alonso, J. L. Revealing the multiple structures of serine. Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 20183−20188. (7) Häber, T.; Seefeld, K.; Engler, G.; Grimme, S.; Kleinermanns, K. IR/UV spectra and quantum chemical calculations of Trp-Ser: Stacking interactions between backbone and indole side-chain. Phys. Chem. Chem. Phys. 2008, 10, 2844−2851. (8) Fricke, H.; Funk, A.; Schrader, T.; Gerhards, M. Investigation of secondary structure elements by IR/UV double resonance spectroscopy: Analysis of an isolated beta-sheet model system. J. Am. Chem. Soc. 2008, 130, 4692−4698. (9) López, J. C.; Alonso, J. L.; Peña, I.; Vaquero, V. Hydrogen bonding and structure of uracil-water and thymine-water complexes. Phys. Chem. Chem. Phys. 2010, 12, 14128−14134. (10) Peña, I.; Sanz, M. E.; López, J. C.; Alonso, J. L. Preferred conformers of proteinogenic glutamic acid. J. Am. Chem. Soc. 2012, 134, 2305−2312. (11) Clarkson, J. R.; Baquero, E.; Shubert, V. A.; Myshakin, E. M.; Jordan, K. J.; Zwier, T. S. Laser-initiated shuttling of a water molecule between H-bonding sites. Science 2005, 307, 1443−1446. (12) Becucci, M.; Pietraperzia, G.; Pasquini, M.; Piani, G.; Zoppi, A.; Chelli, R.; Castellucci, E.; Demtroeder, W. A study on the anisolewater complex by molecular beam-electronic spectroscopy and molecular mechanics calculations. J. Chem. Phys. 2004, 120, 5601. (13) Piani, G.; Pasquini, M.; Pietraperzia, G.; Becucci, M.; Schiccheri, N.; Biczysko, M.; Pavone, M.; Barone, V. Isotopomeric conformational changes in the anisole-water complex: New insights from HR-UV spectroscopy and theoretical studies. J. Phys. Chem. A 2007, 111, 12363−12371. (14) Biczysko, M.; Piani, G.; Pasquini, M.; Schiccheri, N.; Pietraperzia, G.; Becucci, M.; Pavone, M.; Barone, V. On the properties of microsolvated molecules in the ground (S0) and excited (S1) states: The anisole-ammonia 1:1 complex. J. Chem. Phys. 2007, 127, 144303. (15) Pietraperzia, G.; Pasquini, M.; Schiccheri, N.; Piani, G.; Becucci, M.; Castellucci, E.; Biczysko, M.; Bloino, J.; Barone, V. The gas phase anisole dimer: A combined high-resolution spectroscopy and computational study of a stacked molecular system. J. Phys. Chem. A 2009, 113, 14343−14351. (16) Schmitt, M.; Bhom, M.; Ratzer, C.; Vu, C.; Kalkman, I.; Meerts, W. L. Structural selection by microsolvation: A conformational locking of tryptamine. J. Am. Chem. Soc. 2005, 127, 10356−10364. (17) Melandri, S. “Union is strength”: How weak hydrogen bonds become strong. Phys. Chem. Chem. Phys. 2011, 13, 13901−13911. (18) Snoek, L. C.; Kroemer, R. T.; Hockridge, M. R.; Simons, J. P. Conformational landscapes of aromatic amino acids in the gas phase: Infrared and ultraviolet ion dip spectroscopy of tryptophan. Phys. Chem. Chem. Phys. 2001, 3, 1819. (19) Reimann, B.; Buchold, K.; Barth, H. D.; Brutschy, B.; Tarakeshwar, P.; Kim, K. S. Anisole-(H2O)n (n=1,3) complexes: An experimental and theoretical investigation of the modulation of optimal structures, binding energies, and vibrational spectra in both the ground and first excited states. J. Chem. Phys. 2002, 117, 8805. (20) Ribblett, J. W.; Sinclair, W. E.; Borst, D. R.; Yi, J. T.; Pratt, D. W. High Resolution electronic spectra of anisole and anisole-water in the gas phase: Hydrogen bond switching in the S1 state. J. Phys. Chem. A 2006, 110, 1478−1483. (21) Gordy, W.; Cook, R. L. In Microwave Molecular Spectra, 3rd ed.; Weissberger, A., Ed.; Wiley: New York, 1984.

CONCLUDING REMARKS In the present paper a thorough investigation of the equilibrium structure and the molecular and spectroscopic properties of the W1 2-thiouracil−water complex is reported. For the first time, its molecular structure has been determined by means of highlevel quantum-chemical calculations proved to provide structural parameters with an estimated accuracy of about 0.002 Å for bond distances and of about 0.1° for angles. Furthermore, this is the first application of the so-called “cheap” computational composite scheme,41,58,60,79 purposely set up for accurately describing the electronic structure and spectroscopic properties of small biomolecules, to a weakly bonded molecular complex. The results reported demonstrated the suitability of this approach also for accurately studying molecular complexes. The binding energy and the spectroscopic parameters required in the field of rotational spectroscopy have also been determined by means of a composite scheme analogous to that introduced for the evaluation of equilibrium geometry. Our best-estimated, zero-point corrected binding energy is 32.2 kJ mol−1 and can be considered a reliable reference value, also fulfilling the chemical accuracy requirements. Concerning the spectroscopic parameters, the experiment−theory comparison available for 2-thiouracil leads to a conservative uncertainty of about 0.1% for our predicted rotational constants of the vibrational ground state, whereas errors on the order of 3% are expected for quartic centrifugal-distortion and nitrogen quadrupole-coupling constants. On the basis of the comparison of experimental and computed 2-thiouracil spectra (see ref 41 and Figure 3), the rotational transitions of the complex are expected to be conservatively predicted with uncertainties ranging from 0.05% to 0.2%.

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ASSOCIATED CONTENT

S Supporting Information *

Equilibrium structure information: the Z-matrix employed in our calculations together with the geometrical parameters obtained for all the computational levels considered. This material is available free of charge via the Internet at http:// pubs.acs.org

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AUTHOR INFORMATION

Corresponding Author

*C. Puzzarini. E-mail: [email protected]. Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS This work was supported by Italian MIUR (PRIN 2012 “STAR: Spectroscopic and computational Techniques for Astrophysical and atmospheric Research” and PON01-01078/8) and by the University of Bologna (RFO funds). The high performance computer facilities of the DREAMS center (http://dreamshpc. sns.it) are acknowledged for providing computer resources. The support of COST CMTS-Action CM1002 “COnvergent Distributed Environment for Computational Spectroscopy (CODECS)” is also acknowledged.

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Molecular Structure and Spectroscopic Parameters of the Thiouracil

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