Fully ab initio IR spectra for complex molecular systems from perturbative vibrational approaches: Glycine as a test case

First-Principles Calculations for Glycine Adsorption Dynamics and Surface-Enhanced Raman Spectroscopy on Diamond Surfaces

Based on first-principles calculations, the stability of three adsorption configurations of glycine on the (100) surface of diamonds was studied, leading to an investigation into the surface-enhanced Raman scattering (SERS) effect of the diamond substrate. The results showed that the carboxyl-terminated adsorption configuration (CAR) was the most stable and shortest interface distance compared to other configurations. This stability was primarily attributed to the formation of strong polar covalent bonds between the carboxyl O atoms and the surface C atoms of the (100) surface of diamonds. These results were further corroborated by first-principles molecular dynamics simulations. Within the temperature range of 300 to 500 K, the glycine molecules in the carboxyl-terminated adjacent-dimer phenyl-like (CAR) configuration exhibited only simple thermal vibrations with varying amplitudes. In contrast, the metastable ATO and carboxyl-terminated trans-dimer phenyl-like ring (CTR) configurations were observed to gradually transform into benzene-ring-like structures akin to the CAR configuration. After adsorption, the intensity of glycine's characteristic peaks increased substantially, accompanied by a blue shift phenomenon. Notably, the characteristic peaks related to the carboxyl and amino groups exhibited the highest enhancement amplitude, exceeding 200 times, with an average enhancement amplitude exceeding 50 times. The diamond substrate, with its excellent adsorption properties and strong surface Raman spectroscopy characteristics, represents a highly promising candidate in the field of biomedicine.

Analysis of the NMR Parameters Shielding and Spin-Spin Coupling Constants of Glycine Conformers

In this study, we worked at the CCSD/aug-cc-pVTZ level to obtain the conformers of glycine in its neutral and zwitterionic forms in the gas and water phases. We then computed the NMR properties (spin-spin coupling constants and nuclear magnetic shieldings) at the SOPPA/aug-cc-pVTZ-J level. We attempt to elucidate the apparent discrepancy arising from two previous works by Valverde et al. [J. Chem. Phys., 2018, 148, 024305] and Caputo and Provasi [Sci, 2021, 3, 41]. Our optimized structures align with previous theoretical predictions, although some geometries were not found. Additionally, our results suggest that in the gas phase the Δ 1J(O,C) = 1J(Ocis,CO) - 1J(Otrans,CO) is positive when the acid group is in the trans conformation and negative in the cis conformation; however, this trend is not well reproduced in water. From magnetic shielding calculations, we cannot distinguish between an O-H in the cis or trans conformation.

Harmonic and anharmonic vibrational computations for biomolecular building blocks: Benchmarking DFT and basis sets by theoretical and experimental IR spectrum of glycine conformers

Advanced vibrational spectroscopic experiments have reached a level of sophistication that can only be matched by numerical simulations in order to provide an unequivocal analysis, a crucial step to understand the structure-function relationship of biomolecules. While density functional theory (DFT) has become the standard method when targeting medium-size or larger systems, the problem of its reliability and accuracy are well-known and have been abundantly documented. To establish a reliable computational protocol, especially when accuracy is critical, a tailored benchmark is usually required. This is generally done over a short list of known candidates, with the basis set often fixed a priori. In this work, we present a systematic study of the performance of DFT-based hybrid and double-hybrid functionals in the prediction of vibrational energies and infrared intensities at the harmonic level and beyond, considering anharmonic effects through vibrational perturbation theory at the second order. The study is performed for the six-lowest energy glycine conformers, utilizing available "state-of-the-art" accurate theoretical and experimental data as reference. Focusing on the most intense fundamental vibrations in the mid-infrared range of glycine conformers, the role of the basis sets is also investigated considering the balance between computational cost and accuracy. Targeting larger systems, a broad range of hybrid schemes with different computational costs is also tested.

A time averaged semiclassical approach to IR spectroscopy

We propose a new semiclassical approach to the calculation of molecular IR spectra. The method employs the time averaging technique of Kaledin and Miller upon symmetrization of the quantum dipole-dipole autocorrelation function. Spectra at high and low temperatures are investigated. In the first case, we are able to point out the possible presence of hot bands in the molecular absorption line shape. In the second case, we are able to reproduce accurate IR spectra as demonstrated by a calculation of the IR spectrum of the water molecule, which is within 4% of the exact intensity. Our time averaged IR spectra can be directly compared to time averaged semiclassical power spectra as shown in an application to the CO2 molecule, which points out the differences between IR and power spectra and demonstrates that our new approach can identify active IR transitions correctly. Overall, the method features excellent accuracy in calculating absorption intensities and provides estimates for the frequencies of vibrations in agreement with the corresponding power spectra. In perspective, this work opens up the possibility to interface the new method with the semiclassical techniques developed for power spectra, such as the divide-and-conquer one, to get accurate IR spectra of complex and high-dimensional molecular systems.

Theoretical Simulation of Near-Infrared Spectrum of Piperine: Insight into Band Origins and the Features of Regression Models

We investigated the near-infrared spectrum of piperine using quantum mechanical calculations. We evaluated two efficient approaches, DVPT2//PM6 and DVPT2//ONIOM [PM6:B3LYP/6-311++G(2df, 2pd)] that yielded a simulated spectrum with varying accuracy versus computing time factor. We performed vibrational assignments and unveiled complex nature of the near-infrared spectrum of piperine, resulting from a high level of band convolution. The most meaningful contribution to the near-infrared absorption of piperine results from binary combination bands. With the available detailed near-infrared assignment of piperine, we interpreted the properties of partial least square regression models constructed in our earlier study to describe the piperine content in black pepper samples. Two models were compared with spectral data sets obtained with a benchtop and a miniaturized spectrometer. The two spectrometers implement distinct technology which leads to a profound instrumental difference and discrepancy in the predictive performance when analyzing piperine content. We concluded that the sensitivity of the two instruments to certain types of piperine vibrations is different and that the benchtop spectrometer unveiled higher selectivity. Such difference in obtaining chemical information from a sample can be one of the reasons why the benchtop spectrometer performs better in analyzing the piperine content of black pepper. This evidenced direct correspondence between the features critical for applied near-infrared spectroscopic routine and the underlying vibrational properties of the analyzed constituent in a complex sample.

MULTIMODE Calculations of Vibrational Spectroscopy and 1d Interconformer Tunneling Dynamics in Glycine Using a Full-Dimensional Potential Energy Surface

A full-dimensional, permutationally invariant polynomial potential energy surface for glycine recently reported (R. Conte et al., J. Chem. Phys. 2020, 153, 244301) is used with the code MULTIMODE to determine the IR absorption spectra for Conformers I and II using a new separable dipole moment function. The calculated spectra agree well with the experimental ones. The full-dimensional nature of the potential allows us also to examine dynamical results, such as tunneling rates. Remarkably, using a one-dimensional path based on the potential energy surface to estimate the tunneling rate from Conformer VI to Conformer I, good agreement is found with the recent experimental measurement. Finally a brief comparison of our potential energy surface with a recently reported sGDML one is made.

Chiral Inversion of Amino Acids in Antiparallel β-Sheets at Interfaces Probed by Vibrational Sum Frequency Generation Spectroscopy

A parallel study of protein variants with all (l-), all (d-), or mixed (l-)/(d-) amino acids can be used to assess how backbone architecture versus side chain identity determines protein structure. Here, we investigate the secondary structure and side chain orientation dynamics of the antiparallel β-sheet peptide LK7β (Ac-Leu-Lys-Leu-Lys-Leu-Lys-Leu-NH2) composed of all (l-), all (d-), or alternating (l-Leu)/(d-Lys) amino acids. Using interface-selective vibrational sum frequency generation spectroscopy (VSFG), we observe that the alternating (l-)/(d-) peptide lacks a resonant C-H stretching mode compared to the (l-) and (d-) variants and does not form antiparallel β-sheets. We rationalize our observations on the basis of density functional theory calculations and molecular dynamics (MD) simulations of LK7β at the air-water interface. Irrespective of the handedness of the amino acids, leucine side chains prefer to orient toward the hydrophobic air phase while lysine side chains prefer the hydrophilic water phase. These preferences dictate the backbone configuration of LK7β and thereby the folding of the peptide. Our MD simulations show that the preferred side chain orientations can force the backbone of a single strand of (l-) LK7β at the air-water interface to adopt β-sheet Ramachandran angles. However, denaturation of the β-sheets at pH = 2 results in a negligible chiral VSFG amide I response. The combined computational and experimental results lend critical support to the theory that a chiral VSFG response requires macroscopic chirality, such as in β-sheets. Our results can guide expectations about the VSFG optical responses of proteins and should improve understanding of how amino acid chirality modulates the structure and function of natural and de novo proteins at biological interfaces.

Spectra-Structure Correlations in Isotopomers of Ethanol (CX3CX2OX; X = H, D): Combined Near-Infrared and Anharmonic Computational Study

The effect of isotopic substitution on near-infrared (NIR) spectra has not been studied in detail. With an exception of few major bands, it is difficult to follow the spectral changes due to complexity of NIR spectra. Recent progress in anharmonic quantum mechanical calculations allows for accurate reconstruction of NIR spectra. Taking this opportunity, we carried out a systematic study of NIR spectra of six isotopomers of ethanol (CX₃CX₂OX; X = H, D). Besides, we calculated the theoretical spectra of two other isotopomers (CH₃CD₂OD and CD₃CH₂OD) for which the experimental spectra are not available. The anharmonic calculations were based on generalized vibrational second-order perturbation theory (GVPT2) at DFT and MP2 levels with several basis sets. We compared the accuracy and efficiency of various computational methods. It appears that the best results were obtained with B2PLYP-GD3BJ/def2-TZVP//CPCM approach. Our simulations included the first and second overtones, as well as binary and ternary combinations bands. This way, we reliably reproduced even minor bands in the spectra of diluted samples (0.1 M in CCl₄). On this basis, the effect of isotopic substitution on NIR spectra of ethanol was accurately reproduced and comprehensively explained.

"Divide and conquer" semiclassical molecular dynamics: A practical method for spectroscopic calculations of high dimensional molecular systems

We extensively describe our recently established "divide-and-conquer" semiclassical method [M. Ceotto, G. Di Liberto, and R. Conte, Phys. Rev. Lett. 119, 010401 (2017)] and propose a new implementation of it to increase the accuracy of results. The technique permits us to perform spectroscopic calculations of high-dimensional systems by dividing the full-dimensional problem into a set of smaller dimensional ones. The partition procedure, originally based on a dynamical analysis of the Hessian matrix, is here more rigorously achieved through a hierarchical subspace-separation criterion based on Liouville's theorem. Comparisons of calculated vibrational frequencies to exact quantum ones for a set of molecules including benzene show that the new implementation performs better than the original one and that, on average, the loss in accuracy with respect to full-dimensional semiclassical calculations is reduced to only 10 wavenumbers. Furthermore, by investigating the challenging Zundel cation, we also demonstrate that the "divide-and-conquer" approach allows us to deal with complex strongly anharmonic molecular systems. Overall the method very much helps the assignment and physical interpretation of experimental IR spectra by providing accurate vibrational fundamentals and overtones decomposed into reduced dimensionality spectra.

Semiclassical "Divide-and-Conquer" Method for Spectroscopic Calculations of High Dimensional Molecular Systems

A new semiclassical "divide-and-conquer" method is presented with the aim of demonstrating that quantum dynamics simulations of high dimensional molecular systems are doable. The method is first tested by calculating the quantum vibrational power spectra of water, methane, and benzene-three molecules of increasing dimensionality for which benchmark quantum results are available-and then applied to C_{60}, a system characterized by 174 vibrational degrees of freedom. Results show that the approach can accurately account for quantum anharmonicities, purely quantum features like overtones, and the removal of degeneracy when the molecular symmetry is broken.

On-the-Fly ab Initio Semiclassical Calculation of Glycine Vibrational Spectrum

We present an on-the-fly ab initio semiclassical study of vibrational energy levels of glycine, calculated by Fourier transform of the wavepacket correlation function. It is based on a multiple coherent states approach integrated with monodromy matrix regularization for chaotic dynamics. All four lowest-energy glycine conformers are investigated by means of single-trajectory semiclassical spectra obtained upon classical evolution of on-the-fly trajectories with harmonic zero-point energy. For the most stable conformer I, direct dynamics trajectories are also run for each vibrational mode with energy equal to the first harmonic excitation. An analysis of trajectories evolved up to 50 000 atomic time units demonstrates that, in this time span, conformers II and III can be considered as isolated species, while conformers I and IV show a pretty facile interconversion. Therefore, previous perturbative studies based on the assumption of isolated conformers are often reliable but might be not completely appropriate in the case of conformer IV and conformer I for which interconversion occurs promptly.

The VN3H defect in diamond: a quantum-mechanical characterization

The structural, electronic, energetic and vibrational spectroscopic (IR and Raman) properties of the VN₃H defect in diamond are investigated with quantum mechanical simulations.

Spectroscopic and Computational Study of Acetic Acid and Its Cyclic Dimer in the Near-Infrared Region

Anharmonic vibrational analysis of near-infrared (NIR) spectra of acetic acid was carried out by anharmonic quantum chemical calculation in a wide concentration range of its CCl4 solution. By predicting vibrational spectra of acetic acid for the first time over a wide NIR region, it was possible to elucidate the influence of the formation of acetic acid cyclic dimer on its NIR spectrum. Quantum chemical simulations were based on coupled cluster and density functional theory quantum methods. Additionally, Møller-Plesset perturbation theory was employed for the additional calculation of hydrogen bonding stabilization energies. An anharmonic vibrational analysis was performed with the use of generalized second-order vibrational perturbation theory (GVPT2). A hybrid approach was assumed, in which monomeric species was treated by CCSD(T)/aug-cc-pVDZ (harmonic approximation) and B3LYP/SNSD (anharmonic approximation) methods. For the cyclic dimer, B3LYP and B2PLYP single and double hybrid functionals, paired with an SNSD basis set, were employed. DFT calculations were augmented with additional empirical dispersion correction. It was found that quantum chemically calculated vibrational modes in the NIR region are in a good agreement with experimental data. The results of anharmonic vibrational analysis were supported by a harmonic shift analysis, for elucidating the very strong anharmonic coupling observed between stretching modes of hydrogen bonded bridge in the cyclic dimer. However, the calculated wavenumbers for combination modes of double hydrogen bonded bridge in the cyclic dimer, which are very sensitive to the formation of hydrogen bonding, were found to be underestimated by quantum chemical methods. Therefore, by band fitting, the wavenumbers and shape parameters for these bands were found, and the modeled spectra were adjusted accordingly. A high accuracy of simulated spectra was achieved, and a detailed analysis of the experimental NIR spectra of acetic acid was possible, with successful identification of numerous experimental bands, including those which originate from concentration effects. It was also found that the main spectral features observed in the NIR spectra of carboxylic acid upon the formation of hydrogen bond should be accounted for combination modes of the stretching and bending vibrations of double hydrogen-bonded bridge in the cyclic dimers of acetic acid.

A spectroscopic and theoretical study in the near-infrared region of low concentration aliphatic alcohols

The near-infrared (NIR) spectra of low-concentration (5 × 10⁻³ M) solutions in CCl₄ of basic aliphatic alcohols, methanol, ethanol, and 1-propanol were, for the first time, calculated by second-order vibrational perturbation theory computations and were compared with the corresponding experimental data.

Silver colloid and film substrates in surface-enhanced Raman scattering for 2-thiouracil detection

Surface-enhanced Raman scattering-based silver substrates were designed and fabricated for the detection of 2-thiouracil (2-TU).

New insights into the vibrational and optical signatures of trans-stilbene via integrated experimental and quantum mechanical approaches

The structure, spectroscopic parameters and optical properties of stilbene have been investigated by a computational protocol including suitable treatment of anharmonic contributions together with new experimental results.

CC/DFT Route toward Accurate Structures and Spectroscopic Features for Observed and Elusive Conformers of Flexible Molecules: Pyruvic Acid as a Case Study

The structures and relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semiexperimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.001 Å and 0.1 deg for bond lengths and angles, respectively. Highly accurate relative energies of all conformers (Tc-, Tt-, and Ct-PA) and of the transition states connecting them are provided along with the thermodynamic properties at low and high temperatures, thus leading to conformational enthalpies accurate to 1 kJ mol(-1). Concerning microwave spectroscopy, rotational constants accurate to about 20 MHz are provided for the Tt- and Ct-PA conformers, together with the computed centrifugal-distortion constants and dipole moments required to simulate their rotational spectra. For Ct-PA, vibrational frequencies in the mid-infrared region accurate to 10 cm(-1) are reported along with theoretical estimates for the transitions in the near-infrared range, and the corresponding infrared spectrum including fundamental transitions, overtones, and combination bands has been simulated. In addition to the new data described above, theoretical results for the Tc- and Tt-PA conformers are compared with all available experimental data to further confirm the accuracy of the hybrid coupled-cluster/density functional theory (CC/DFT) protocol applied in the present study. Finally, we discuss in detail the accuracy of computational models fully based on double-hybrid DFT functionals (mainly at the B2PLYP/aug-cc-pVTZ level) that avoid the use of very expensive CC calculations.

Largely reduced grid densities in a vibrational self-consistent field treatment do not significantly impact the resultingwavenumbers

Especially for larger molecules relevant to life sciences, vibrational self-consistent field (VSCF) calculations can become unmanageably demanding even when only first and second order potential coupling terms are considered. This paper investigates to what extent the grid density of the VSCF’s underlying potential energy surface can be reduced without sacrificing accuracy of the resulting wavenumbers. Including single-mode and pair contributions, a reduction to eight points per mode did not introduce a significant deviation but improved the computational efficiency by a factor of four. A mean unsigned deviation of 1.3% from the experiment could be maintained for the fifteen molecules under investigation and the approach was found to be applicable to rigid, semi-rigid and soft vibrational problems likewise. Deprotonated phosphoserine, stabilized by two intramolecular hydrogen bonds, was investigated as an exemplary application.

Accurate molecular structures and infrared spectra of trans-2,3-dideuterooxirane, methyloxirane, and trans-2,3-dimethyloxirane

Oxirane derivatives are the most used benchmarks for chiroptical spectroscopies in view of their small size and relative rigidity. The molecular structure, vibrational harmonic and anharmonic frequencies, and infrared intensities of the ground electronic states are analyzed in this paper. Equilibrium structure and harmonic force fields have been evaluated by means of high-level quantum-chemical calculations at the coupled-cluster level including single and double excitations together with a perturbative treatment of triples (CCSD(T)). Extrapolation to the complete basis-set limit as well as core-correlation effects have also been taken into account. Anharmonic contributions have been computed at the CCSD(T)/cc-pVTZ level for trans-2,3-dideuterooxirane. These data can serve as references to evaluate the accuracy of less expensive computational approaches rooted in the density functional theory (DFT). The latter have been used within hybrid CC/DFT approaches, which have been applied to simulate fully anharmonic infrared (IR) spectra. Finally, the best theoretical estimates of the equilibrium structures and vibrational wavenumbers are compared to the most accurate experimental data and show in all cases very good agreement, i.e., within 0.001 Å, 0.1 deg, 10 cm(-1), and 0.5 km mol(-1), for bond lengths, angles, wavenumbers, and IR intensities, respectively.

An integrated experimental and quantum-chemical investigation on the vibrational spectra of chlorofluoromethane

The vibrational analysis of the gas-phase infrared spectra of chlorofluoromethane (CH2ClF, HCFC-31) was carried out in the range 200-6200 cm(-1). The assignment of the absorption features in terms of fundamental, overtone, combination, and hot bands was performed on the medium-resolution (up to 0.2 cm(-1)) Fourier transform infrared spectra. From the absorption cross section spectra accurate values of the integrated band intensities were derived and the global warming potential of this compound was estimated, thus obtaining values of 323, 83, and 42 on a 20-, 100-, and 500-year horizon, respectively. The set of spectroscopic parameters here presented provides the basic data to model the atmospheric behavior of this greenhouse gas. In addition, the obtained vibrational properties were used to benchmark the predictions of state-of-the-art quantum-chemical computational strategies. Extrapolated complete basis set limit values for the equilibrium geometry and harmonic force field were obtained at the coupled-cluster singles and doubles level of theory augmented by a perturbative treatment of triple excitations, CCSD(T), in conjunction with a hierarchical series of correlation-consistent basis sets (cc-pVnZ, with n = T, Q, and 5), taking also into account the core-valence correlation effects and the corrections due to diffuse (aug) functions. To obtain the cubic and quartic semi-diagonal force constants, calculations employing second-order Møller-Plesset perturbation (MP2) theory, the double-hybrid density functional B2PLYP as well as CCSD(T) were performed. For all anharmonic force fields the performances of two different perturbative approaches in computing the vibrational energy levels (i.e., the generalized second order vibrational treatment, GVPT2, and the recently proposed hybrid degeneracy corrected model, HDCPT2) were evaluated and the obtained results allowed us to validate the spectroscopic predictions yielded by the HDCPT2 approach. The predictions of the deperturbed second-order perturbation approach, DVPT2, applied to the computation of infrared intensities beyond the double-harmonic approximation were compared to the accurate experimental values here determined. Anharmonic DFT and MP2 corrections to CCSD(T) intensities led to a very good agreement with the absorption cross section measurements over the whole spectral range here analysed.

Anharmonic theoretical simulations of infrared spectra of halogenated organic compounds

The recent implementation of the computation of infrared (IR) intensities beyond the double-harmonic approximation [J. Bloino and V. Barone, J. Chem. Phys. 136, 124108 (2012)] paved the route to routine calculations of infrared spectra for a wide set of molecular systems. Halogenated organic compounds represent an interesting class of molecules, from both an atmospheric and computational point of view, due to the peculiar chemical features related to the halogen atoms. In this work, we simulate the IR spectra of eight halogenated molecules (CH2F2, CHBrF2, CH2DBr, CF3Br, CH2CHF, CF2CFCl, cis-CHFCHBr, cis-CHFCHI), using two common hybrid and double-hybrid density functionals in conjunction with both double- and triple-ζ quality basis sets (SNSD and cc-pVTZ) as well as employing the coupled-cluster theory with basis sets of at least triple-ζ quality. Finally, we compare our results with available experimental spectra, with the aim of checking the accuracy and the performances of the computational approaches.

A second-order perturbation theory route to vibrational averages and transition properties of molecules: general formulation and application to infrared and vibrational circular dichroism spectroscopies

A general formulation to compute anharmonic vibrational averages and transition properties at the second-order of perturbation theory is derived from the Rayleigh-Schrödinger development. This approach is intended to be applicable to any property expanded as a Taylor series up to the third order with respect to normal coordinates or their associated momenta. The equations are straightforward to implement and can be easily adapted to various properties, as illustrated for the case of electric and magnetic dipole moments. From those, infrared and vibrational circular dichroism spectra can be readily obtained. This fully automatic procedure has been applied to several chiral molecules of small-to-medium sizes and compared to the standard double harmonic approximation and to experimental data.