Quantum chemical calculation of vibrational spectra of large molecules--Raman and IR spectra for Buckminsterfullerene

In this work we demonstrate how different modern quantum chemical methods can be efficiently combined and applied for the calculation of the vibrational modes and spectra of large molecules. We are aiming at harmonic force fields, and infrared as well as Raman intensities within the double harmonic approximation, because consideration of higher order terms is only feasible for small molecules. In particular, density functional methods have evolved to a powerful quantum chemical tool for the determination of the electronic structure of molecules in the last decade. Underlying theoretical concepts for the calculation of intensities are reviewed, emphasizing necessary approximations and formal aspects of the introduced quantities, which are often not explicated in detail in elementary treatments of this topic. It is shown how complex quantum chemistry program packages can be interfaced to new programs in order to calculate IR and Raman spectra. The advantages of numerical differentiation of analytical gradients, dipole moments, and static, as well as dynamic polarizabilities, are pointed out. We carefully investigate the influence of the basis set size on polarizabilities and their spatial derivatives. This leads us to the construction of a hybrid basis set, which is equally well suited for the calculation of vibrational frequencies and Raman intensities. The efficiency is demonstrated for the highly symmetric C(60), for which we present the first all-electron density functional calculation of its Raman spectrum.     

The structure and the Raman vibrational spectrum of the beryllium aquacation

The experimental Raman vibrational spectrum of the 5.94 m water solution of the beryllium(II) chloride has been acquired. Theoretical frequencies, infrared and Raman intensities of the vibrational spectrum of the beryllium cation tetrahydrate have been calculated by means of quantum chemical approach. The peaks of the experimental spectrum have been assigned on the basis of the results of the quantum-chemical calculations. It has been shown that the hydrating surrounding of the aquacation increases effectively the frequency of the beryllium-oxygen stretching vibration by 16% in comparison with the free complex.     

Evaluation of range-separated hybrid density functionals for the prediction of vibrational frequencies, infrared intensities, and Raman activities

We present an assessment of different density functionals, with emphasis on range-separated hybrids, for the prediction of fundamental and harmonic vibrational frequencies, infrared intensities, and Raman activities. Additionally, we discuss the basis set convergence of vibrational properties of H2O with long-range corrected hybrids. Our results show that B3LYP is the best functional for predicting vibrational frequencies (both fundamental and harmonic); the screened-PBE hybrid (HSE) density functional works best for infrared intensities, and the long-range corrected PBE (LC-omegaPBE), M06-HF, and M06-L density functionals are almost as good as MP2 for predicting Raman activities. We show the predicted Raman spectrum of adenine as an example of a medium-size molecule where a DFT/Sadlej pVTZ calculation is affordable and compare our results against the experimental spectrum.     

A spectroscopic and computational investigation of the vanadomolybdate local structure in the lyonsite phase Mg(2.5)VMoO(8)

The vibrational spectrum of Mg2.5VMoO8 obtained by quantum mechanical simulation is compared with the experimentally observed Raman spectrum. This simulation suggests that the observed band at 1016 cm(-1) is attributed to the Mo=O-Mg stretching from two-coordinate oxygen atoms that are adjacent to Mg2+ cation vacancies. Extended X-ray absorption fine structure spectroscopy supports the structural model used to simulate the vibrational modes in Mg2.5VMoO8 that match the observed Raman data.     

Calculation of Raman optical activity spectra of methyl-β-D-glucose incorporating a full molecular dynamics simulation of hydration effects

We report calculations of the Raman and Raman optical activity (ROA) spectra of methyl-β-D-glucose utilizing density functional theory combined with molecular dynamics (MD) simulations to provide an explicit hydration environment. This is the first report of such combination of MD simulations with ROA ab initio calculations. We achieve a significant improvement in accuracy over the more commonly used gas phase and polarizable continuum model (PCM) approaches, resulting in an excellent level of agreement with the experimental spectrum. Modeling the ROA spectra of carbohydrates has until now proven a notoriously difficult challenge due to their sensitivity to the effects of hydration on the molecular vibrations involving each of the chiral centers. The details of the ROA spectrum of methyl-β-D-glucose are found to be highly sensitive to solvation effects, and these are correctly predicted for the first time including those originating from the highly sensitive low frequency vibrational modes. This work shows that a thorough consideration of the role of water is pivotal for understanding the vibrational structure of carbohydrates and presents a new and powerful tool for characterizing carbohydrate structure and conformational dynamics in solution.     

Vibrational analysis of hydroxyacetone

In order to be able to fully understand the vibrational dynamics of monosaccharide sugars, we started with hydroxyacetone CH2OHCOCH3, and glycolaldehyde CH2OHCOH, which are among the smallest molecules that contain hydroxyl and carbonyl group on neighboring carbon atoms. This sterical configuration is characteristic for saccharides and determines their biochemical activity. In this work vibrational analysis of hydroxyacetone was undertaken by performing the normal coordinate analysis for glycolaldehyde first, and transferring these force constants to hydroxyacetone. The observed Raman and infrared bands for 90 wt.% solution of hydroxyacetone in water (acetol) were used as a first approximation for the bands of free hydroxyacetone. The number of observed Raman and infrared bands for acetol exceeds the number of calculated values for the most stable hydroxyacetone conformer with Cs symmetry, which suggests more than one conformer of hydroxyacetone in water solution. In particular, there are two bands both in infrared (1083 and 1057 cm(-1)) and in Raman spectrum (1086.5 and 1053 cm(-1)) that are assigned to the CO stretching mode and this is one of the indicators of several hydroxyacetone conformers in the solution. Additional information was obtained from low temperature Raman spectra: at 240 K a broad asymmetric band centered around 280 cm(-1) appears, suggesting a disorder in the orientation of hydroxyl groups. Glassy state forms at approximately 150K. The broad band at 80 cm(-1) is assigned to frozen torsions of hydroxymethyl groups.     

Observation of molecules adsorbed on III-V semiconductor quantum dots by surface-enhanced Raman scattering

I report for the first time surface-enhanced Raman scattering (SERS) from molecules adsorbed on InAs/GaAs quantum dots. This result is very interesting because previous SERS experiments have been essentially restricted to molecules adsorbed on metallic surfaces. Raman scattering from pyridine molecules adsorbed on these III-V quantum dots structures is strongly enhanced relative to the same molecules in solution. The most interesting feature in the SERS spectrum is the appearance of a new vibrational band. I suggest that this line should be attributed to the chemisorbed pyridine that is formed by coordination of its lone pair electrons of the N atom to the semiconductor surface. This work provides unambiguous experimental evidence for SERS on III-V semiconductor quantum dots. Nanostructures are currently considered as potential building blocks for nanodevices. The performance and reliability of these devices strongly depend on the surface and interfacial properties of the constituent nanomaterials. Therefore, this work illustrates the considerable potential of SERS spectroscopy as a powerful new tool in nanoscience.     

DFT and Raman spectroscopy of porphyrin derivatives: Tetraphenylporphine (TPP)

Raman spectrum of the meso tetraphenylporphine (TPP) deposited onto smooth copper surface as thin film were recorded in the region 200–1700 cm⁻¹. To investigate the effect of meso-phenyl substitution rings on the vibrational spectrum of free base porphyrin, we calculated Raman and infrared (IR) spectra of the meso-tetraphenylporphine (TPP), meso tetramethylporphine (TMP), copper (II)porphine (CuPr) and free base porphine (FBP) at the B3LYP/6-311+G(d,p) level of the density functional theory (DFT). The observed Raman spectrum of the TPP is assigned based on the calculated its Raman spectrum in connection with the calculated spectra of the TMP, CuPr and FBP by taking into account of their corresponding vibrational motions of the Raman modes of frequencies. Results of the calculations clearly indicated that the meso tetraphenyl substitution rings are totally responsible for the observed Raman bands at ∼1593, 1234 and 1002 cm⁻¹. The calculated and observed Raman spectra also suggested that the observed Raman band with a medium intense at 962 cm⁻¹ might result from the surface plasmon effect. Furthermore, the observed Raman bands with medium intense at ∼334 and ∼201 cm⁻¹ are as results of the dimerization or aggregation of the TPP or would be that related to intramolecular interaction. We also calculated IR spectra of these molecules at same level of the theory. To investigate the solvent effect on the vibrational spectrum of porphine, the Raman and IR spectra of the TPP and FBP are calculated in solution phase where water used as solvent. The results of these calculation indicated that there is no any significant effect on the vibrational spectrum of the TPP.     

Role of hydration in determining the structure and vibrational spectra of L-alanine and N-acetyl L-alanine N′-methylamide in aqueous solution: a combined theoretical and experimental approach

In this work we have utilized recent density functional theory Born-Oppenheimer molecular dynamics simulations to determine the first principles locations of the water molecules in the first solvation shell which are responsible for stabilizing the zwitterionic structure of L-alanine. Previous works have used chemical intuition or classical molecular dynamics simulations to position the water molecules. In addition, a complete shell of water molecules was not previously used, only the water molecules which were thought to be strongly interacting (H-bonded) with the zwitterionic species. In a previous work by Tajkhorshid et al. (J Phys Chem B 102:5899) the L-alanine zwitterion was stabilized by 4 water molecules, and a subsequent work by Frimand et al. (Chem Phys 255:165) the number was increased to 9 water molecules. Here we found that 20 water molecules are necessary to fully encapsulate the zwitterionic species when the molecule is embedded within a droplet of water, while 11 water molecules are necessary to encapsulate the polar region with the methyl group exposed to the surface, where it migrates during the MD simulation. Here we present our vibrational absorption, vibrational circular dichroism and Raman and Raman optical activity simulations, which we compare to the previous simulations and experimental results. In addition, we report new VA, VCD, Raman and ROA measurements for L-alanine in aqueous solution with the latest commercially available FTIR VA/VCD instrument (Biotools, Jupiter, FL, USA) and Raman/ROA instrument (Biotools). The signal to noise of the spectra of L-alanine measured with these new instruments is significantly better than the previously reported spectra. Finally we reinvestigate the causes for the stability of the P_π structure of the alanine dipeptide, also called N-acetyl-L-alanine N′-methylamide, in aqueous solution. Previously we utilized the B3LYP/6-31G* + Onsager continuum level of theory to investigate the stability of the NALANMA4WC Han et al. (J Phys Chem B 102:2587) Here we use the B3PW91 and B3LYP hybrid exchange correlation functionals, the aug-cc-pVDZ basis set and the PCM and CPCM (COSMO) continuum solvent models, in addition to the Onsager and no continuum solvent model. Here by the comparison of the VA, VCD, Raman and ROA spectra we can confirm the stability of the NALANMA4WC due to the strong hydrogen bonding between the four water molecules and the peptide polar groups. Hence we advocate the use of explicit water molecules and continuum solvent treatment for all future spectral simulations of amino acids, peptides and proteins in aqueous solution, as even the structure (conformer) present cannot always be found without this level of theory. Festschift in Honor of Philip J. Stephens’ 65th Birthday. During the proof stage of this article a very relevant article has been published by M. Losada and Y. Xu titled “Chirality transfer through hydrogen-bonding: Experimental and ab initio analyses of vibrational circular dichroism spectra of methyl lactate in water” in Phys Chem Chem Phys 2007, 9: 3127–3135. In that work they confirm that the effects of water are seen in the VCD spectra and hence it is fundamental to include explicit water molecules in modeling studies of the vibrational spectra of biomolecules in aqueous solution.     

Tip-enhanced Raman spectroscopy for nanoscale strain characterization

Tip-enhanced Raman spectroscopy (TERS), which utilizes the strong localized optical field generated at the apex of a metallic tip when illuminated, has been shown to successfully probe the vibrational spectrum of today’s and tomorrow’s state-of-the-art silicon and next-generation semiconductor devices, such as quantum dots. Collecting and analyzing the vibrational spectrum not only aids in material identification but also provides insight into strain distributions in semiconductors. Here, the potential of TERS for nanoscale characterization of strain in silicon devices is reviewed. Emphasis will be placed on the key challenges of obtaining spectroscopic images of strain in actual strained silicon devices. Figure Figure Concept of Tip Enhanced Raman Spectroscopy (TERS), which utilizes the strong localized optical field generated at the apex of a metallic tip when illuminated. TERS has been demonstrated to successfully probe the vibrational spectrum of today’s and tomorrow’s state-of-the-art silicon and next generation semiconductor devices     

Chiral terpenes in different phases: <Emphasis Type="Italic">R</Emphasis>-(−)-camphorquinone studied by IR–Raman–VCD spectroscopies and theoretical calculations

R-(−)-camphorquinone is a bicyclical terpenoid with many usages and application in different fields. Different experimental and theoretical works reveal that there is only one stable conformer of this chiral chemical species in agreement to the sterical restriction that the bicycle introduces. In the current work, from a complete assignment of the vibrational IR and Raman spectra, we are able to explain the VCD spectrum of the title compound. The recorded spectra of R-(−)-camphorquinone in different phases have been analyzed and compared: the first one in CCl₄ solution, the second one using Nujol and Fluorolube suspensions and the third one using thin films. Finally, to study the coupling between the two C=O stretching normal modes, a NBO analysis is performed. The present work reveals that IR, Raman and VCD, combined with quantum chemical calculations, are helpful complementary techniques to characterize chiral systems, as terpenes, in different phases.     

Nuclear quantum effect and temperature dependency on the hydrogen‐bonded structure of base pairs

The structure of Watson–Crick‐type adenine‐thymine and guanine‐cytosine pairs has been studied by hybrid Monte Carlo (HMC) and path integral hybrid Monte Carlo (PIHMC) simulations with the use of semiempirical PM6‐DH+ method in the gas phase. We elucidated the nuclear quantum effect and temperature dependency on the hydrogen‐bonded moiety of base pairs. It was shown that the contribution of nuclear quantum effect on the hydrogen‐bonded structure is significant not only at low temperature 150 K but also at temperature as high as 450 K. The relative position of hydrogen‐bonded proton between two heavy atoms and the nuclear quantum nature of the proton are also shown. Furthermore, we have applied principal component analysis to HMC and PIHMC simulations to analyze the nuclear quantum effect on intermolecular motions. We found that the ratio of Buckle mode (lowest vibrational mode from normal mode analysis) decreases due to the nuclear quantum effect, whereas that of Propeller mode (second lowest vibrational mode) increases. In addition, nonplanar structures of base pairs were found to become stable due to the nuclear quantum effect from two‐dimensional free energy landscape along Buckle and Propeller modes. © 2013 Wiley Periodicals, Inc.     

Lagrangian approach to molecular vibrational Raman intensities using time-dependent hybrid density functional theory

The authors propose a new route to vibrational Raman intensities based on analytical derivatives of a fully variational polarizability Lagrangian. The Lagrangian is constructed to recover the negative frequency-dependent polarizability of time-dependent Hartree-Fock or adiabatic (hybrid) density functional theory at its stationary point. By virtue of the variational principle, first-order polarizability derivatives can be computed without using derivative molecular orbital coefficients. As a result, the intensities of all Raman-active modes within the double harmonic approximation are obtained at approximately the same cost as the frequency-dependent polarizability itself. This corresponds to a reduction of the scaling of computational expense by one power of the system size compared to a force constant calculation and to previous implementations. Since the Raman intensity calculation is independent of the harmonic force constant calculation more, computationally demanding density functionals or basis sets may be used to compute the polarizability gradient without much affecting the total time required to compute a Raman spectrum. As illustrated for fullerene C60, the present approach considerably extends the domain of molecular vibrational Raman calculations at the (hybrid) density functional level. The accuracy of absolute and relative Raman intensities of benzene obtained using the PBE0 hybrid functional is assessed by comparison with experiment.     

The structure of the hydrated electron. Part 2. A mixed quantum/classical molecular dynamics embedded cluster density functional theory: single-excitation configuration interaction study

Adiabatic mixed quantum/classical (MQC) molecular dynamics (MD) simulations were used to generate snapshots of the hydrated electron in liquid water at 300 K. Water cluster anions that include two complete solvation shells centered on the hydrated electron were extracted from the MQC MD simulations and embedded in a roughly 18 Ax18 Ax18 A matrix of fractional point charges designed to represent the rest of the solvent. Density functional theory (DFT) with the Becke-Lee-Yang-Parr functional and single-excitation configuration interaction (CIS) methods were then applied to these embedded clusters. The salient feature of these hybrid DFT(CIS)/MQC MD calculations is significant transfer (approximately 18%) of the excess electron's charge density into the 2p orbitals of oxygen atoms in OH groups forming the solvation cavity. We used the results of these calculations to examine the structure of the singly occupied and the lower unoccupied molecular orbitals, the density of states, the absorption spectra in the visible and ultraviolet, the hyperfine coupling (hfcc) tensors, and the infrared (IR) and Raman spectra of these embedded water cluster anions. The calculated hfcc tensors were used to compute electron paramagnetic resonance (EPR) and electron spin echo envelope modulation (ESEEM) spectra for the hydrated electron that compared favorably to the experimental spectra of trapped electrons in alkaline ice. The calculated vibrational spectra of the hydrated electron are consistent with the red-shifted bending and stretching frequencies observed in resonance Raman experiments. In addition to reproducing the visible/near IR absorption spectrum, the hybrid DFT model also accounts for the hydrated electron's 190-nm absorption band in the ultraviolet. Thus, our study suggests that to explain several important experimentally observed properties of the hydrated electron, many-electron effects must be accounted for: one-electron models that do not allow for mixing of the excess electron density with the frontier orbitals of the first-shell solvent molecules cannot explain the observed magnetic, vibrational, and electronic properties of this species. Despite the need for multielectron effects to explain these important properties, the ensemble-averaged radial wavefunctions and energetics of the highest occupied and three lowest unoccupied orbitals of the hydrated electrons in our hybrid model are close to the s- and p-like states obtained in one-electron models. Thus, one-electron models can provide a remarkably good approximation to the multielectron picture of the hydrated electron for many applications; indeed, the two approaches appear to be complementary.     

The specific vibrational modes of GTP in solution and bound to Ras: a detailed theoretical analysis by QM/MM simulations

The hydrolysis of guanosine triphosphate (GTP) in general, and especially by GTPases like the Ras protein, is in the focus of biological investigations. A huge amount of experimental data from Fourier-transformed infrared studies is currently available, and many vibrational bands of free GTP, GTP·Mg(2+), and Ras·GTP·Mg(2+) in solution have been assigned by isotopic labeling. In the Ras environment, bands between 800 cm(-1) and 1300 cm(-1) have already been assigned, but not those below 800 cm(-1). The combination of quantum and molecular mechanics (QM/MM) methods takes the quantum effects for selected relevant atoms into account. This provides structural details, vibrational frequencies and electron distributions of the region of interest. We therefore used MM and QM/MM simulations to investigate the normal vibrational modes of GTP, GTP·Mg(2+), and Ras·GTP·Mg(2+) in solution, and assigned the vibrational frequencies for each normal vibration mode. In this study, the quantum box contains the nucleoside and the Mg(2+). The comparison of calculated and experimental vibrational spectra provides a very good control for the quality of the calculations. Structurally, MM and QM/MM simulations reveal a stable tridentate coordination of the Mg(2+) by GTP in water, and a stable bidentate coordination by GTP in complex with Ras. For validation, we compare the calculated frequencies and isotopic shifts with the experimental results available in the range of 800 cm(-1) to 1300 cm(-1). For the first time we suggest band assignments of the vibrational modes below 800 cm(-1) by comparison of calculated and experimental spectra.     

Initial excited-state structural dynamics of thymine are coincident with the expected photochemical dynamics

To explore the excited-state structural dynamics of thymine, a DNA nucleobase, we measured the resonance Raman spectra of thymine in aqueous solution at wavelengths throughout the lowest-energy absorption band. Self-consistent analysis of the resulting resonance Raman excitation profiles and absorption spectrum using a time-dependent wave packet formalism yielded the excited-state structural dynamics. The photochemically relevant C=C stretching and C-H deformation vibrational modes were found to exhibit maximum resonance Raman intensity and structural change upon photoexcitation for thymine, suggesting that the initial dynamics of thymine lie along the photochemical reaction coordinate.     

Spectroscopic investigation of a new hybrid glass formed by the interaction between croconate ion and calcium polyphosphate

In this work, a new organic-inorganic hybrid material has been synthesized by the incorporation of croconate ion into a calcium polyphosphate coacervate. The hybrid so obtained was characterized by means of electronic and vibrational spectroscopies. The material is a homogeneous mixture described by a structural model, which includes helical chains of polyphosphate ions, where the calcium ion occupies the internal vacancies of the structure. The croconate ion appears to be occupying the regions outside the polymeric structure, surrounded by several water molecules. The electronic spectrum of the incorporated material shows a broad band peaking at the same wavelength region (363 nm) observed for the aqueous solution of croconate ion, and manifesting the Jahn-Teller effect as evidenced by the doublet structure of the band. The infrared spectrum is widely dominated by the absorption bands of the polyphosphate ion and the appearance of the carbonyl stretching band at ca. 1550 cm(-1) indicates the presence of croconate ion incorporated in the structure. The Raman spectrum of the material shows several vibrational bands related to the oxocarbon moiety; most of them are shifted in comparison with the free ion. These shifts can be understood in terms of strong hydrogen bonding interactions between water molecules and the oxocarbon moiety. The low temperature methodology proposed here can be well used in the preparation of new phosphate glasses containing organic moieties opening the route to an entirely new class of hybrid glasses.     

Spin-Phonon Coupling and Slow-Magnetic Relaxation in Pristine Ferrocenium

We report the spin dynamic properties of non-substituted ferrocenium complexes. Ferrocenium shows a field-induced single-molecule magnet behaviour in DMF solution while cobaltocene lacks slow spin relaxation neither in powder nor in solution. Multireference quantum mechanical calculations give a non-Aufbau orbital occupation for ferrocenium with small first excitation energy that agrees with the relatively large measured magnetic anisotropy for a transition metal S=1/2 system. The analysis of the spin relaxation shows an important participation of quantum tunnelling, Raman, direct and local-mode mechanisms which depend on temperature and the external field conditions. The calculation of spin-phonon coupling constants for the vibrational modes shows that the first vibrational mode, despite having a low spin-phonon constant, is the most efficient process for the spin relaxation at low temperatures. In such conditions, vibrational modes with higher spin-phonon coupling constants are not populated. Additionally, the vibrational energy of this first mode is in excellent agreement with the experimental fitted value obtained from the local-mode mechanism.     

Vibrational spectroscopic studies and ab initio calculations of a substituted amide of pyrazine-2-carboxylic acid--C12H10ClN3O

A substituted amide of pyrazine-2-carboxylic acid was prepared and the IR spectrum is recorded and analysed. The vibrational frequencies and corresponding vibrational assignments are examined theoretically using the Gaussian03 set of quantum chemistry codes. Predicted infrared and Raman intensities are reported.