Vibrational computations beyond the harmonic approximation: Performances of the B3LYP density functional for semirigid molecules

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.

Investigation of cathinone analogs targeting human dopamine transporter using molecular modeling

In a step towards understanding the structure-property relationship among Synthetic Cathinones (SCs), a combined methodology based on Density Functional Theory (DFT), Administration, Distribution, Metabolism, Excretion, and Toxicity (ADMET) predictions, docking and molecular dynamics simulations have been applied to correlate physicochemical descriptors of various SCs to their biological activity. The results from DFT and molecular docking studies correlate well with each other explaining the biological activity trends of the studied SCs. Quantum mechanical descriptors viz. polarizability, electron affinity, ionization potential, chemical hardness, electronegativity, molecular electrostatic potential, and ion interaction studies unravel the distinguishingly reactive nature of Group D (pyrrolidine substituted) and Group E (methylenedioxy and pyrrolidine substituted) compounds. According to ADMET analysis, Group D and Group E molecules have a higher probability of permeating through the blood-brain barrier. Molecular docking results indicate that Phe76, Ala77, Asp79, Val152, Tyr156, Phe320, and Phe326 constitute the binding pocket residues of hDAT in which the most active ligands MDPV, MDPBP, and MDPPP are bound. Finally, to validate the derived quantum chemical descriptors and docking results, Molecular Dynamics (MD) simulations are performed with homology-modelled hDAT (human dopamine transporter). The MD simulation results revealed that the majority of SCs remain stable within the hDAT protein's active sites via non-bonded interactions after 100 ns long simulations. The findings from DFT, ADMET analysis, molecular docking, and molecular dynamics simulation studies complement each other suggesting that pyrrolidine-substituted SCs (Group D and E), specifically, MPBP and PVN are proven potent SCs along with MDPV, validating various experimental observations.Communicated by Ramaswamy H. Sarma.

From the Automated Calculation of Potential Energy Surfaces to Accurate Infrared Spectra

Advances in the development of quantum chemical methods and progress in multicore architectures in computer science made the simulation of infrared spectra of isolated molecules competitive with respect to established experimental methods. Although it is mainly the multidimensional potential energy surface that controls the accuracy of these calculations, the subsequent vibrational structure calculations need to be carefully converged in order to yield accurate results. As both aspects need to be considered in a balanced way, we focus on approaches for molecules of up to 12-15 atoms with respect to both parts, which have been automated to some extent so that they can be employed in routine applications. Alternatives to machine learning will be discussed, which appear to be attractive, as long as local regions of the potential energy surface are sufficient. The automatization of these methods is still in its infancy, and the generalization to molecules with large amplitude motions or molecular clusters is far from trivial, but many systems relevant for astrophysical studies are already in reach.

A hydrogen bonding based SERS method for direct label-free L-hydroxyproline detection

The detection of non-protein nitrogen adulterants is a major challenge in dairy testing. As a marker molecule of animal hydrolyzed protein, the presence of non-edible L-hydroxyproline (L-Hyp) molecules can be used to identify low-quality milk containing components of animal hydrolyzed protein. However, it is still difficult to detect L-Hyp directly in milk. The Ag@COF-COOH substrate in this paper can be used to realize label-free L-Hyp sensitive detection based on the hydrogen bond transition mechanism. To explore the mechanism, the binding sites of hydrogen bond interaction have been verified experimentally and computationally, and the charge transfer process was also explained in terms of HOMO/LOMO energy level. In conclusion, the quantitative models for L-Hyp in an aqueous environment and in milk were developed. The limit of detection (LOD) of L-Hyp in an aqueous environment could reach 8.18 ng/mL, with R² of 0.982. The linear range of quantitative detection in milk was 0.5-1000 μg/mL and the LOD was as low as 0.13 μg/mL. In this work, a hydrogen bond interaction based Surface-enhanced Raman spectroscopy (SERS) method for the label-free detection of L-Hyp was proposed, which complemented the application of SERS technology in the detection of dairy products.

Time Resolved Raman Scattering of Molecules: A Quantum Mechanics Approach with Stochastic Schroedinger Equation

Raman scattering is a very powerful tool employed to characterize molecular systems. Here we propose a novel theoretical strategy to calculate the Raman cross-section in time domain, by computing the cumulative Raman signal emitted during the molecular evolution in time. Our model is based on a numerical propagation of the vibronic wave function under the effect of a light pulse of arbitrary shape. This approach can therefore tackle a variety of experimental setups. Both resonance and nonresonance Raman scattering can be retrieved, and also the time-dependent fluorescence emission is computed. The model has been applied to porphyrin considering both resonance and nonresonance conditions and varying the incident field duration. Moreover the effect of the vibrational relaxation, which should be taken into account when its time scale is similar to that of the Raman emission, has been included through the stochastic Schroedinger equation approach.

Calculating bond dissociation energies of X-H (X=C, N, O, S) bonds of aromatic systems via density functional theory: a detailed comparison of methods

In this study, the performance of 17 different density functional theory functionals was compared for the calculation of the bond dissociation energy (BDE) values of X-H (X=C, N, O, S) bonds of aromatic compounds. The effect of the size of the basis set (expansions of 6-31(G)) was also assessed for the initial geometry and zero-point energy calculations, followed by the single-point BDE calculations with different model chemistries with the 6-311 + (3df,2p) basis set. It was found that the size of the basis set for geometry optimization has a much smaller effect on the accuracy of BDE than the choice of functional for the following single-point calculations. The M06-2X, M05-2X and M08-HX functionals yielded highly accurate BDE values compared to experimental data (with the average mean unsigned error MUE = 1.2-1.5 kcal mol^-1), performing better than any of the other functionals. The results suggest that geometry optimization may be performed with B3LYP functional and a small basis set, whereas the M06-2X, M05-2X and M08-HX density functionals with a suitably large basis set offer the best method for calculating BDEs of ArX-H (X=C, N, O, S) bonds.

Relativistic Four-Component DFT Calculations of Vibrational Frequencies

We investigate the effect of relativity on harmonic vibrational frequencies. Density functional theory (DFT) calculations using the four-component Dirac–Coulomb Hamiltonian have been performed for 15 hydrides (H₂X, X = O, S, Se, Te, Po; XH₃, X = N, P, As, Sb, Bi; and XH₄, X = C, Si, Ge, Sn, Pb) as well as for HC≡CPbH₃. The vibrational frequencies have been calculated using finite differences of the molecular energy with respect to geometrical distortions of the nuclei. The influences of the choice of basis set, exchange–correlation functional, and step length for the numerical differentiation on the calculated harmonic vibrational frequencies have been tested, and the method has been found to be numerically robust. Relativistic effects are noticeable for the heavier congeners H₂Te and H₂Po, SbH₃ and BiH₃, and SnH₄ and PbH₄ and are much more pronounced for the vibrational modes with higher frequencies. Spin–orbit effects constitute a very small fraction of the total relativistic effects, except for H₂Te and H₂Po. For HC≡CPbH₃ we find that only the frequencies of the modes with large contributions from Pb displacements are significantly affected by relativity.

Nano-porous C4N as a toxic pesticide's scavenger: A quantum chemical approach

The sensing affinity of C₄N is the most fascinating topic of research due to its excellent chemical and electronic properties. Moreover, owing to the highly active porous cavity, C₄N can easily accommodate foreign molecules. Herein, we studied the adsorption properties of carbamate insecticides (CMs) namely, Dimetalin (DMT), Carbanolate (CBT), Isolan (ISO) and Propoxur (PRO) using density functional theory calculations. All the results are calculated at widely accepted ωB97XD functional along with 6-31G(d, p) basis set. The calculated counterpoise corrected interaction energy of the reported complexes ranges between -20.05 and -27.04 kcal/mol, however, the interaction distances are found to be higher than 2.00 Å. The values of interacting parameters depict that the carbamate molecules are physisorbed via noncovalent interactions that can easily be reversible. Moreover, the binding of selected insecticides notably changes the electronic structure of C₄N. The electronic changes are characterized by the energies of HOMO & LUMO, their energy gaps and CHELPG charge transfer. The charge density difference between C₄N surface and carbamate pesticides are characterized by EDD and CDA analysis. Moreover, the ab initio molecular dynamic study reveals that the complexes are stable even at 500 K. The photochemical sensing properties of C₄N are estimated by time dependent UV-Vis calculations. The high sensitivity of C₄N towards considered analytes enable it to act as a promising sensor for toxic pesticides.

Structural and Vibrational Properties of Amino Acids from Composite Schemes and Double-Hybrid DFT: Hydrogen Bonding in Serine as a Test Case

The structures, relative stabilities, and vibrational wavenumbers of the two most stable conformers of serine, stabilized by the O-H···N, O-H···O═C and N-H···O-H intramolecular hydrogen bonds, have been evaluated by means of state-of-the-art composite schemes based on coupled-cluster (CC) theory. The so-called "cheap" composite approach (CCSD(T)/(CBS+CV)^MP2) allowed determination of accurate equilibrium structures and harmonic vibrational wavenumbers, also pointing out significant corrections beyond the CCSD(T)/cc-pVTZ level. These accurate results stand as a reference for benchmarking selected hybrid and double-hybrid, dispersion-corrected DFT functionals. B2PLYP-D3 and DSDPBEP86 in conjunction with a triple-ζ basis set have been confirmed as effective methodologies for structural and spectroscopic studies of medium-sized flexible biomolecules, also showing intramolecular hydrogen bonding. These best performing double-hybrid functionals have been employed to simulate IR spectra by means of vibrational perturbation theory, also considering hybrid CC/DFT schemes. The best overall agreement with experiment, with mean absolute error of 8 cm^-1, has been obtained by combining CCSD(T)/(CBS+CV)^MP2 harmonic wavenumbers with B2PLYP-D3/maug-cc-pVTZ anharmonic corrections. Finally, a composite scheme entirely based on CCSD(T) calculations (CCSD(T)/CBS+CV) has been employed for energetics, further confirming that serine II is the most stable conformer, also when zero-point vibrational energy corrections are included.

General Perturb-Then-Diagonalize Model for the Vibrational Frequencies and Intensities of Molecules Belonging to Abelian and Non-Abelian Symmetry Groups

In this paper, we show that the standard second-order vibrational perturbation theory (VPT2) for Abelian groups can be used also for non-Abelian groups without employing specific equations for two- or threefold degenerate vibrations but rather handling in the proper way all the degeneracy issues and deriving the peculiar spectroscopic signatures of non-Abelian groups (e.g., l -doubling) by a posteriori transformations of the eigenfunctions. Comparison with the results of previous conventional implementations shows a perfect agreement for the vibrational energies of linear and symmetric tops, thus paving the route to the transparent extension of the equations already available for asymmetric tops to the energies of spherical tops and the infrared and Raman intensities of molecules belonging to non-Abelian symmetry groups. The whole procedure has been implemented in our general engine for vibro-rotational computations beyond the rigid rotor/harmonic oscillator model and has been validated on a number of test cases.

Unusual binary aggregates of perylene bisimide revealed by their electronic transitions in helium nanodroplets and DFT calculations

The S1 ← S0 electronic transition of perylene bisimide (PBI) and its binary aggregates were investigated using a combination of helium nanodroplet isolation spectroscopy and computational methods. First, well-resolved vibronic bands of the PBI monomer obtained under the superfluid helium nanodroplet environment were compared to simulated vibronic spectra with anharmonic corrections of the band positions. Second, about ten sets of weaker vibronic bands were observed, which show similar vibronic patterns as that of the PBI monomer and have their band origins red-shifted by about 8 to 218 cm-1. Experimental Poisson curve analyses, performed at the origins of these new sets of bands and the PBI monomer, indicate that the carriers of these weaker red-shifted vibronic bands are binary adducts of PBI. Three types of PBI dimer structures where the electronic transition dipole moments of the two subunits are perpendicular to each other were proposed as possible carriers of these red-shifted vibronic patterns. Extensive vibronic simulations were carried out in a multi-step procedure with TD-DFT, vertical Hessian, and finally adiabatic Hessian approaches. Small red-shifted band origins and very similar vibronic patterns to that of the monomer were predicted for unusual, T-shaped, type I dimer structures and are in close agreement with the experimental data. The combined experimental and theoretical results indicate that the helium nanodroplet environment enables the formation of these unusual T-shaped dimers and stabilizes them.

Towards a complete elucidation of the ro-vibrational band structure in the SF6 infrared spectrum from full quantum-mechanical calculations

The first accurate and complete theoretical room-temperature rotationally resolved spectra in the range 300-3000 cm-1 are reported for the three most abundant isotopologues (32SF6, 33SF6 and 34SF6) of the sulfur hexafluoride molecule. The literature reports that SF6 is widely used as a prototype molecule for studying the multi-photon excitation processes with powerful lasers in the infrared range. On the other hand, SF6 is an important greenhouse molecule with a very long lifetime in the atmosphere. Because of relatively low vibrational frequencies, the hot bands of this molecule contribute significantly to the absorption infrared spectra even at room temperature. This makes the calculation of complete rovibrational line lists required for fully converged opacity modeling extremely demanding. In order to reduce the computational costs, symmetry was exploited at all stages of the first global variational nuclear motion calculations by means of irreducible tensor operators. More than 2600 new vibrational band centers were predicted using our empirically refined ab initio potential energy surface. Highly excited rotational states were calculated up to J = 121, resulting in 6 billion transitions computed from an ab initio dipole moment surface and distributed over more than 500 cold and hot bands. The final line lists are made available through the TheoReTS information system (http://theorets.univ-reims.fr, http://theorets.tsu.ru). For the first time, the major (ro)vibrational band structures in the wavenumber range corresponding to the strongest absorption in the infra-red are completely elucidated for a seven-atom molecule, providing excellent agreement with the observed spectral patterns. It is shown that the obtained results are more complete than all available line lists, permitting reliable modelling of the temperature dependence of the molecular opacity.

Transfer Learning to CCSD(T): Accurate Anharmonic Frequencies from Machine Learning Models

The calculation of the anharmonic modes of small- to medium-sized molecules for assigning experimentally measured frequencies to the corresponding type of molecular motions is computationally challenging at sufficiently high levels of quantum chemical theory. Here, a practical and affordable way to calculate coupled-cluster quality anharmonic frequencies using second-order vibrational perturbation theory (VPT2) from machine-learned models is presented. The approach, referenced as "NN + VPT2", uses a high-dimensional neural network (PhysNet) to learn potential energy surfaces (PESs) at different levels of theory from which harmonic and VPT2 frequencies can be efficiently determined. The NN + VPT2 approach is applied to eight small- to medium-sized molecules (H₂CO, trans-HONO, HCOOH, CH₃OH, CH₃CHO, CH₃NO₂, CH₃COOH, and CH₃CONH₂) and frequencies are reported from NN-learned models at the MP2/aug-cc-pVTZ, CCSD(T)/aug-cc-pVTZ, and CCSD(T)-F12/aug-cc-pVTZ-F12 levels of theory. For the largest molecules and at the highest levels of theory, transfer learning (TL) is used to determine the necessary full-dimensional, near-equilibrium PESs. Overall, NN + VPT2 yields anharmonic frequencies to within 20 cm^-1 of experimentally determined frequencies for close to 90% of the modes for the highest quality PES available and to within 10 cm^-1 for more than 60% of the modes. For the MP2 PESs only ∼60% of the NN + VPT2 frequencies were within 20 cm^-1 of the experiment, with outliers up to ∼150 cm^-1, compared to the experiment. It is also demonstrated that the approach allows to provide correct assignments for strongly interacting modes such as the OH bending and the OH torsional modes in formic acid monomer and the CO-stretch and OH-bend mode in acetic acid.

Theoretical Characterization of the Structure and Spectroscopy of HCNO2 Isomers and Applications

We carried out a theoretical, fully ab initio, investigation of the stable forms of the [H,C,N,O,O] pentatomic molecular system, whose isomers are involved in fundamental combustion and atmospheric processes and are of potential interest for astrophysics. By adopting the MP2 and CCSD(T) electronic structure methods, combined with extrapolations to the complete basis set (CBS) limit, we characterized 20 low-energy isomers, excluding weak van der Waals complexes. For these molecules, we determined a set of geometrical parameters, relative energies, anharmonic vibrational frequencies, IR intensities, and fragmentation/formation energies from various atomic and/or molecular fragments. We discuss the relevance of the present findings for the search of new molecular species in astrophysical and atmospheric media and give suggestions for their possible detection in laboratory experiments. The set of data provided by the present work should facilitate the identification of these species from their gas-phase and low-temperature solid matrix spectra, whenever measured.

Characterization of the simplest sulfenyl thiocyanate: isomers, spectroscopy and implications of astrophysical and biological relevance

Sulfenyl thiocyanate compounds, RSSCN, are involved in the human immune system biochemical processes. They are also the routes for the synthesis of complex S-containing species such as polypeptides, or symmetrical (RSSR) and unsymmetrical disulfides (RSSR'). At present, we have characterized the stable forms of the simplest sulfenyl thiocyanate compound, HSSCN, at the coupled cluster level. We found twenty-three isomers, for which we determined a set of structural parameters, anharmonic frequencies and reaction energies for the formation of the corresponding diatomic + triatomic and atomic + tetratomic fragments. We also discussed the implications of the present findings for biological entities containing a disulfide bridge, where we identified three isomers that may serve as prototypes. Similarities and differences with other S/N hybrid bioactive molecules are also discussed. From an astrophysical point of view, we expect HSSCN isomers to be present in astrophysical media, since several of their molecular fragments have already been detected. In sum, the present set of data can be used for the identification of HSSCN compounds and understanding the physical chemistry of sulfur containing molecules in vivo, in the laboratory and in astrophysical media.

Calculation of Anharmonic IR and Raman Intensities for Periodic Systems from DFT Calculations: Implementation and Validation

An extension of the CRYSTAL program is presented allowing for calculations of anharmonic infrared (IR) intensities and Raman activities for periodic systems. This work is a follow-up of two papers devoted to the computation of anharmonic vibrational states of solids from DFT (density functional theory) calculations (Erba et al. J. Chem. Theory Comput. 2019, 15, 3755-3765 and Erba et al. J. Chem. Theory Comput. 2019, 15, 3766-3777). The approach presented here relies on the evaluation of integrals of the dipole moment and polarizability operators over anharmonic wave functions obtained from either VSCF (vibrational self-consistent field) or VCI (vibrational configuration interaction) calculations. With this extension, the program now allows for a more complete characterization of the vibrational spectroscopic features of solids within the density functional theory. In particular, it is able (i) to provide reliable positions and intensities for the most intense spectral features and (ii) to check whether a first overtone or a combination band has a nonvanishing IR intensity or Raman activity. Therefore, it becomes possible to assign the transition(s) corresponding to satellite peak(s) around a fundamental transition or the overtones or combination bands that may be as intense as their corresponding fundamental transitions through the strongest mode-mode couplings, as in so-called Fermi resonances. The present method is assessed on two molecular systems, H₂O and H₂CO, as well as on two solid state cases, boron hydrides BH₄ and their deuterated species BD₄ in a crystalline environment of alkali metals (M = Na, K). The solid state cases are particularly insightful as, in the B-H (or B-D) stretching region here considered, they exhibit many spectral features entirely due to anharmonic effects: two out of three in the IR spectrum and four out of six in the Raman spectrum. All IR and Raman active overtones and combination bands experimentally observed are correctly predicted with our approach. The effect of the adopted quantum-chemical model (DFT exchange-correlation functional/basis set) for the electronic structure calculations on the computed spectra is discussed and found to be significant, which suggests some special care is needed for the analysis of subtle spectral features.

Vibrations of the guanine-cytosine pair in chloroform: an anharmonic computational study

We compute at the anharmonic level the vibrational spectra of the Watson-Crick dimer formed by guanosine (G) and cytidine (C) in chloroform, together with those of G, C and the most populated GG dimer. The spectra for deuterated and partially deuterated GC are also computed. We use DFT calculations, with B3LYP and CAM-B3LYP as reference functionals. Solvent effects from chloroform are included via the Polarizable Continuum Model (PCM), and by performing tests on models including up two chloroform molecules. Both B3LYP and CAM-B3LYP calculations reproduce the shape of the experimental spectra well in the fingerprint region (1500-1700 cm-1) and in the N-H stretching region (2800-3600 cm-1), with B3LYP providing better quantitative agreement with experiments. According to our calculations, the N-H amido streching mode of G falls at ∼2900 cm-1, while the N-H amino of G and C falls at ∼3100 cm-1 when hydrogen-bonded, or ∼3500 cm-1 when free. Overtone and combination bands strongly contribute to the absorption band at ∼3300 cm-1. Inclusion of bulk solvent effects significantly increases the accuracy of the computed spectra, while solute-solvent interactions have a smaller, though still noticeable, effect. Some key aspects of the anharmonic treatment of strongly vibrationally coupled supermolecular systems and the related methodological issues are also discussed.

NMR and IR Investigations of Strong Intramolecular Hydrogen Bonds

For the purpose of this review, strong hydrogen bonds have been defined on the basis of experimental data, such as OH stretching wavenumbers, νOH, and OH chemical shifts, δOH (in the latter case, after correction for ring current effects). Limits for O-H···Y systems are taken as 2800 > νOH > 1800 cm-1, and 19 ppm > δOH > 15 ppm. Recent results as well as an account of theoretical advances are presented for a series of important classes of compounds such as β-diketone enols, β-thioxoketone enols, Mannich bases, proton sponges, quinoline N-oxides and diacid anions. The O···O distance has long been used as a parameter for hydrogen bond strength in O-H···O systems. On a broad scale, a correlation between OH stretching wavenumbers and O···O distances is observed, as demonstrated experimentally as well as theoretically, but for substituted β-diketone enols this correlation is relatively weak.

Understanding the interplay between the solvent and nuclear rearrangements in the negative solvatochromism of a push–pull flexible quinolinium cation

The main effects (solvation, vibronic progression) affecting the band position and shape of a push–pull flexible quinolinium cation OPA are highlighted.

Resolving the Origins of Crystalline Anharmonicity Using Terahertz Time-Domain Spectroscopy and ab Initio Simulations

Anharmonicity has been shown to be an important piece of the fundamental framework that dictates numerous observable phenomena. In particular, anharmonicity is the driving force of vibrational relaxation processes, mechanisms that are integral to the proper function of numerous chemical processes. However, elucidating its origins has proven difficult due to experimental and theoretical challenges, specifically related to separating the anharmonic contributions from other unrelated effects. While no one technique is particularly suited for providing a complete picture of anharmonicity, by combining multiple complementary methods such a characterization can be made. In this study the role of individual atomic interactions on the anharmonic properties of crystalline purine, the building block of many DNA and RNA nucleobases, is studied by experimental terahertz time-domain spectroscopy and first-principles density functional theory (DFT) and ab initio molecular dynamics simulations (AIMD). In particular, the detailed vibrational information provided by the DFT calculations is used to interpret the atomic origins of anharmonic-related effects as determined by the AIMD calculations, which are in good agreement with the experimental data. The results highlight that anharmonicity is especially pronounced in the intermolecular interactions, particularly along the amine hydrogen bond coordinate, and yields valuable insight into what is similarly observed complex biosystems and crystalline solids.

Reliable vibrational wavenumbers for C=O and N-H stretchings of isolated and hydrogen-bonded nucleic acid bases

The accurate prediction of vibrational wavenumbers for functional groups involved in hydrogen-bonded bridges remains an important challenge for computational spectroscopy. For the specific case of the C=O and N-H stretching modes of nucleobases and their oligomers, the paucity of experimental reference values needs to be compensated by reliable computational data, which require the use of approaches going beyond the standard harmonic oscillator model. Test computations performed for model systems (formamide, acetamide and their cyclic homodimers) in the framework of the second order vibrational perturbation theory (VPT2) confirmed that anharmonic corrections can be safely computed by global hybrid (GHF) or double hybrid (DHF) functionals, whereas the harmonic part is particularly challenging. As a matter of fact, GHFs perform quite poorly and even DHFs, while fully satisfactory for C=O stretchings, face unexpected difficulties when dealing with N-H stretchings. On these grounds, a linear regression for N-H stretchings has been obtained and validated for the heterodimers formed by 4-aminopyrimidine with 6-methyl-4-pyrimidinone (4APM-M4PMN) and by uracil with water. In view of the good performance of this computational model, we have built a training set of B2PLYP-D3/maug-cc-pVTZ harmonic wavenumbers (including linear regression scaling for N-H) for six-different uracil dimers and a validation set including 4APM-M4PMN, one of the most stable hydrogen-bonded adenine homodimers, as well as the adenine-uracil, adenine-thymine, guanine-cytosine and adenine-4-thiouracil heterodimers. Because of the unfavourable scaling of DHF harmonic wavenumbers with the dimensions of the investigated systems, we have optimized a linear regression of B3LYP-D3/N07D harmonic wavenumbers for the training set, which has been next checked against the validation set. This relatively cheap model, which shows very good agreement with experimental data (average errors of about 10 cm(-1)), paves the route toward a reliable analysis of spectroscopic signatures for larger polynucleotides.

Analytic calculations of anharmonic infrared and Raman vibrational spectra

Using a recently developed recursive scheme for the calculation of high-order geometric derivatives of frequency-dependent molecular properties [Ringholm et al., J. Comp. Chem., 2014, 35, 622], we present the first analytic calculations of anharmonic infrared (IR) and Raman spectra including anharmonicity both in the vibrational frequencies and in the IR and Raman intensities. In the case of anharmonic corrections to the Raman intensities, this involves the calculation of fifth-order energy derivatives-that is, the third-order geometric derivatives of the frequency-dependent polarizability. The approach is applicable to both Hartree-Fock and Kohn-Sham density functional theory. Using generalized vibrational perturbation theory to second order, we have calculated the anharmonic infrared and Raman spectra of the non- and partially deuterated isotopomers of nitromethane, where the inclusion of anharmonic effects introduces combination and overtone bands that are observed in the experimental spectra. For the major features of the spectra, the inclusion of anharmonicities in the calculation of the vibrational frequencies is more important than anharmonic effects in the calculated infrared and Raman intensities. Using methanimine as a trial system, we demonstrate that the analytic approach avoids errors in the calculated spectra that may arise if numerical differentiation schemes are used.

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).

Vibrational Fingerprints of Low-Lying Pt(n)P(2n) (n = 1-5) Cluster Structures from Global Optimization Based on Density Functional Theory Potential Energy Surfaces

Vibrational fingerprints of small Pt(n)P(2n) (n = 1-5) clusters were computed from their low-lying structures located from a global exploration of their DFT potential energy surfaces with the GSAM code. Five DFT methods were assessed from the CCSD(T) wavenumbers of PtP2 species and CCSD relative energies of Pt2P4 structures. The eight first Pt(n)P(2n) isomers found are reported. The vibrational computations reveal (i) the absence of clear signatures made by overtone or combination bands due to very weak mechanical and electrical anharmonicities and (ii) some significant and recurrent vibrational fingerprints in correlation with the different PP bonding situations in the Pt(n)P(2n) structures.

Theoretical Study of the X2NO Systems (X = F, Cl, Br, I): Effects of Halogen Substitution on Structural and Spectroscopic Properties

Structural and spectroscopic properties of the X2 NO series of radicals, with X = F, Cl, Br, I, have been computed by the coupled cluster ansatz in conjunction with hierarchical series of basis sets, accounting for, in most cases, core correlation effects and extrapolation to the complete basis set limit. Namely, equilibrium structures, vibrational frequencies, and hyperfine coupling constants have been considered. Methods rooted into the density functional theory have been used to estimate anharmonic and, in conjunction with the polarizable continuum model, environmental effects. The remarkable agreement with the available experimental data, limited to the lighter member of the series, confirms the reliability of our computational approach and suggests that the data for heavier species represent reliable benchmarks for future experimental data and/or cheaper computational methods devised for larger systems.

On the Calculation of Vibrational Frequencies for Molecules in Solution Beyond the Harmonic Approximation

We report some results on the calculation of vibrational spectra of molecules in condensed phase with accounting simultaneously for anharmonicity and solute-solvent interactions, the latter being described by means of the polarizable continuum model (PCM). Density functional theory force fields are employed as well as a new implementation of the PCM cavity and its derivatives. The results obtained for formaldehyde and simple peptide prototypes show that our approach is able to yield a quantitative agreement with experiments for vacuo-to-solvent harmonic and anharmonic frequency shifts.