Solvent effects on Raman optical activity spectra calculated using the polarizable continuum model

Effective fully polarizable QM/MM approaches to compute Raman and Raman Optical Activity spectra in aqueous solution

Raman and Raman Optical Activity (ROA) signals are amply affected by solvent effects, especially in the presence of strongly solute-solvent interactions such as Hydrogen Bonding (HB). In this work, we extend the fully atomistic polarizable Quantum Mechanics/Molecular Mechanics approach, based on the Fluctuating Charges and Fluctuating Dipoles force field to the calculation of Raman and ROA spectra. Such an approach is able to accurately describe specific HB interactions, by also accounting for anisotropic contributions due to the inclusion of fluctuating dipoles. To highlight the potentiality of the novel approach, Raman and ROA spectra of L-Serine and L-Cysteine dissolved in aqueous solution are computed and compared both with alternative theoretical approaches and experimental measurements.

Synthesis, Characterization, Antimicrobial, Density Functional Theory, and Molecular Docking Studies of Novel Mn(II), Fe(III), and Cr(III) Complexes Incorporating 4-(2-Hydroxyphenyl azo)-1-naphthol (Az)

This work synthesized three new CrAz₂, MnAz₂, and FeAz₂ complexes and investigated them using IR, mass, UV spectroscopy, elemental analysis, conductivity and magnetic tests, and thermogravimetric analysis. The azo-ligand, 4-(2-hydroxyphenylAzo)-1-naphthol (Az), couples with metal ions via its nitrogen (in -N=N- bonds) and oxygen (in hydroxyl group) atoms, according to the IR spectra of these complexes. Through thermal examination (TG/TGA), the number and location of water in the complexes were also determined. Density functional theory (DFT) theory is applied to ameliorate the structures of the ligand (Az) and metal complexes and analyze the quantum chemical characteristics of these complexes. The antifungal and antibacterial activity of the ligand and its complexes opposed to several hazardous bacteria and fungi was investigated in vitro. Metal complexes were discovered to have a higher inhibitory impact on some organisms than the free ligand. The MnAz₂ complex exhibited the best activity among the studied materials, whereas the CrAz₂ complex had the lowest. The compounds' binding affinity to the E. coli (PDB ID: 1hnj) structure was predicted using molecular docking. Binding energies were calculated by analyzing protein-substrate interactions. These encouraging findings imply that these chemicals may have physiological effects and may be valuable for a variety of medical uses in the future.

Modeling Complex Solvent Effects on the Optical Rotation of Chiral Molecules: A Combined Molecular Dynamics and Density Functional Theory Study

The challenge of assigning the absolute stereochemical configuration to a chiral compound can be overcome via accurate ab initio predictions of optical rotation, a sensitive molecular property that is further complicated by solvent effects. The solvent's "chiral imprint"-the transfer of the chirality from the solute to the surrounding achiral solvent-is explored here using conformational averaging and time-dependent density-functional theory. These complex solvent effects are taken into account via simple averaging over a molecular dynamics trajectory together with the explicit quantum mechanical consideration of the solvent molecules within the solute's cybotactic region and implicit modeling of the bulk solvent. We consider several axes along which the system's optical rotation varies, including the sampling of the dynamical trajectory, the quality of the one-electron basis set, and the use of continuum solvent models to account for bulk effects.

Effective computational route towards vibrational optical activity spectra of chiral molecules in aqueous solution

A polarizable QM/MM approach to accurately compute the Vibrational Optical Activity (VOA) spectra of chiral systems is proposed and applied to aqueous solutions of (l)-methyl lactate and (S)-glycidol.

Local electric fields and molecular properties in heterogeneous environments through polarizable embedding

In spectroscopies, the local field experienced by a molecule embedded in an environment will be different from the externally applied electromagnetic field, and this difference may significantly alter the response and transition properties of the molecule. The polarizable embedding (PE) model has previously been developed to model the local field contribution stemming from the direct molecule-environment coupling of the electromagnetic response properties of molecules in solution as well as in heterogeneous environments, such as proteins. Here we present an extension of this approach to address the additional effective external field effect, i.e., the manifestations of the environment polarization induced by the external field, which allows for the calculation of properties defined in terms of the external field. Within a response framework, we report calculations of the one- and two-photon absorption (1PA and 2PA, respectively) properties of PRODAN-methanol clusters as well as the fluorescent protein DsRed. Our results demonstrate the necessity of accounting for both the dynamical reaction field and effective external field contributions to the local field in order to reproduce full quantum chemical reference calculations. For the lowest π→π* transition in DsRed, inclusion of effective external field effects gives rise to a 1.9- and 3.5-fold reduction in the 1PA and 2PA cross-sections, respectively. The effective external field is, however, strongly influenced by the heterogeneity of the protein matrix, and the resulting effect can lead to either screening or enhancement depending on the nature of the transition under consideration.

The cavity electromagnetic field within the polarizable continuum model of solvation

Cavity field effects can be defined as the consequences of the solvent polarization induced by the probing electromagnetic field upon spectroscopies of molecules in solution, and enter in the definitions of solute response properties. The polarizable continuum model of solvation (PCM) has been extended in the past years to address the cavity-field issue through the definition of an effective dipole moment that couples to the external electromagnetic field. We present here a rigorous derivation of such cavity-field treatment within the PCM starting from the general radiation-matter Hamiltonian within inhomogeneous dielectrics and recasting the interaction term to a dipolar form within the long wavelength approximation. To this aim we generalize the Göppert-Mayer and Power-Zienau-Woolley gauge transformations, usually applied in vacuo, to the case of a cavity vector potential. Our derivation also allows extending the cavity-field correction in the long-wavelength limit to the velocity gauge through the definition of an effective linear momentum operator. Furthermore, this work sets the basis for the general PCM treatment of the electromagnetic cavity field, capable to describe the radiation-matter interaction in dielectric media beyond the long-wavelength limit, providing also a tool to investigate spectroscopic properties of more complex systems such as molecules close to large nanoparticles.

Where does the Raman optical activity of [Rh(en)3]3+ come from? Insight from a combined experimental and theoretical approach

Raman optical activity (ROA) spectra are measured and calculated for Δ- and Λ-tris-(ethylenediamine)rhodium(iii) chloride in aqueous solution.

Circular dichroism and optical rotation of lactamide and 2-aminopropanol in aqueous solution

The performance of implicit and explicit solvent models (polarizable continuum model (PCM) and microsolvation with positions of water molecules obtained either from molecular dynamics (MD) simulations or quantum mechanical geometry optimization) for calculations of electronic circular dichroism (CD) and optical rotation (OR) is examined for two polar and flexible molecules: lactamide and 2-aminopropanol. The vibrational structure of the CD spectrum is modeled for lactamide. The results are compared with the newly obtained experimental data. The signs of the bands are correctly reproduced using all three methods under investigation and the CAM-B3LYP functional for the CD spectrum of lactamide, but not for 2-aminopropanol. The sign of the calculated optical rotation is correctly predicted by means of PCM, but its magnitude is somewhat underestimated in comparison with experiment for lactamide and overestimated for 2-aminopropanol. To some extent it is rectified by employing explicit hydration. Overall, microsolvation with geometry optimization seems more cost-effective than classical MD, but this is likely to be a consequence of inadequate classical potential and electronic structure model.

Toward Ab Initio Anharmonic Vibrational Circular Dichroism Spectra in the Condensed Phase

The first implementation and calculation of anharmonic VCD rotational strengths for solvated systems is reported. Our approach, rooted in the polarizable continuum model (PCM) and in the second-order vibrational perturbation theory (VPT2), permits not only correction for anharmonicity in the signals associated with fundamental transitions but also calculation of rotational strengths of overtones and combination bands. This allows for a more physically consistent comparison between experiment and calculations together with the analysis of spectral regions dominated by anharmonic effects. The developed model is applied to a few test cases, and the computational outcomes are directly compared with experimental data.

Three types of induced tryptophan optical activity compared in model dipeptides: theory and experiment

The tryptophan (Trp) aromatic residue in chiral matrices often exhibits a large optical activity and thus provides valuable structural information. However, it can also obscure spectral contributions from other peptide parts. To better understand the induced chirality, electronic circular dichroism (ECD), vibrational circular dichroism (VCD), and Raman optical activity (ROA) spectra of Trp-containing cyclic dipeptides c-(Trp-X) (where X = Gly, Ala, Trp, Leu, nLeu, and Pro) are analyzed on the basis of experimental spectra and density functional theory (DFT) computations. The results provide valuable insight into the molecular conformational and spectroscopic behavior of Trp. Whereas the ECD is dominated by Trp π-π* transitions, VCD is dominated by the amide modes, well separated from minor Trp contributions. The ROA signal is the most complex. However, an ROA marker band at 1554 cm(-1) indicates the local χ(2) angle value in this residue, in accordance with previous theoretical predictions. The spectra and computations also indicate that the peptide ring is nonplanar, with a shallow potential so that the nonplanarity is primarily induced by the side chains. Dispersion-corrected DFT calculations provide better results than plain DFT, but comparison with experiment suggests that they overestimate the stability of the folded conformers. Molecular dynamics simulations and NMR results also confirm a limited accuracy of the dispersion-DFT model in nonaqueous solvents. Combination of chiral spectroscopies with theoretical analysis thus significantly enhances the information that can be obtained from the induced chirality of the Trp aromatic residue.

Towards an accurate description of anharmonic infrared spectra in solution within the polarizable continuum model: reaction field, cavity field and nonequilibrium effects

We present a newly developed and implemented methodology to perturbatively evaluate anharmonic vibrational frequencies and infrared (IR) intensities of solvated systems described by means of the polarizable continuum model (PCM). The essential aspects of the theoretical model and of the implementation are described and some numerical tests are shown, with special emphasis towards the evaluation of IR intensities, for which the quality of the present method is compared to other methodologies widely used in the literature. Proper account of an incomplete solvation regime in the treatment of the molecular vibration is also considered, as well as inclusion of the coupling between the solvent and the probing field (cavity field effects). In order to assess the quality of our approach, comparison with experimental findings is reported for selected cases.

Importance of solvation in understanding the chiroptical spectra of natural products in solution phase: garcinia acid dimethyl ester

The optical rotatory dispersion (ORD), electronic circular dichroism (ECD), and vibrational circular dichroism (VCD) spectra of (+)-garcinia acid dimethyl ester have been measured and analyzed by comparison with the corresponding spectra predicted by quantum chemical methods for (2S,3S)-garcinia acid dimethyl ester. For solution-phase calculations the recently developed continuous surface charge polarizable continuum model (PCM) has been used. It is found that gas-phase predictions and PCM predictions at the B3LYP/aug-cc-pVDZ level yield nearly mirror-image ECD spectra in the 190-250 nm region for the same absolute configuration and that gas-phase ECD predictions lead to incorrect absolute configuration. At the CAM-B3LYP/aug-cc-pVDZ level, however, gas-phase predictions and PCM predictions of ECD in the 190-250 nm region are not so different, but PCM predictions provide better agreement with the experimental observations. For carbonyl stretching vibrations, the vibrational band positions predicted at the B3LYP/aug-cc-pVDZ level in gas-phase calculations differ significantly from the corresponding experimentally observed band positions, and this discrepancy has also been corrected by the use of PCM. In addition, the solution-phase VCD predictions provided better agreement (with experimental VCD observations) than gas-phase VCD predictions. These observations underscore the importance of including solvent effects in quantum chemical calculations of chiroptical spectroscopic properties.

Theoretical approaches to the calculation of Raman optical activity spectra

In this article, we will give a brief account of the different approaches that have been presented in the literature for calculating Raman optical activity (ROA) spectra by ab initio methods. We will also outline the general structure of a self-consistent-field-based approach for analytic calculations of ROA spectra, including also contributions from London orbitals. The use of London orbitals ensures that the relevant ROA parameters are gauge origin independent. We will also give an outlook on the future of ab initio calculations of Raman optical activity spectra.

Characterizing aqueous solution conformations of a peptide backbone using Raman optical activity computations

Mounting spectroscopic evidence indicates that alanine predominantly adopts extended polyproline II (PPII) conformations in short polypeptides. Here we analyze Raman optical activity (ROA) spectra of N-acetylalanine-N'-methylamide (Ala dipeptide) in H2O and D2O using density functional theory on Monte Carlo (MC) sampled geometries to examine the propensity of Ala dipeptide to adopt compact right-handed (alpha(R)) and left-handed (alpha(L)) helical conformations. The computed ROA spectra based on MC-sampled alpha(R) and PPII peptide conformations contain all the key spectral features found in the measured spectra. However, there is no significant similarity between the measured and computed ROA spectra based on the alpha(L)- and beta-conformations sampled by the MC methods. This analysis suggests that Ala dipeptide populates the alpha(R) and PPII conformations but no substantial population of alpha(L)- or beta-structures, despite sampling alpha(L)- and beta-structures in our MC simulations. Thus, ROA spectra combined with the theoretical analysis allow us to determine the dominant populated structures. Including explicit solute-solvent interactions in the theoretical analysis is essential for the success of this approach.

Degenerate four-wave mixing in solution by cubic response theory and the polarizable continuum model

We have derived and implemented the solvent contribution to the cubic response function for the polarizable continuum model in its integral equation formulation. The present formulation is valid both at the Hartree-Fock and at the Kohn-Sham density functional levels of theory, because both bear the same formal description of the solvent contribution through an additional additive term in the Hamiltonian operator. This new implementation is used to compute the solvent effect for the degenerate four-wave mixing process on three different classes of heteroaromatic chromophores: (I) triazine, benzoxazole, benzimidazole, and benzothiazole; (II) three benzothiazole derivatives; and (III) three tri-s-triazine derivatives. The results are first discussed in terms of the solvent effects on the calculated property and then compared to experimental data for the substrates of class (I) and (II).

Theoretical Determination of the Vibrational Raman Optical Activity Signatures of Helical Polypropylene Chains

Raman and vibrational Raman optical activity (VROA) spectra of helical conformers of polypropylene chains are simulated using ab initio methods to unravel the relationships between the vibrational signatures and the primary and secondary structures of the chains. For a polypropylene chain containing three units, conformational effects are shown to lead to more acute signatures for VROA than for Raman spectra. In addition to regular polypropylene chains, which can display right and left helicities with the same probability, chirality and therefore helicity are enforced by substituting one chain end with a phenyl group. The simulations predict that the threefold helical structures, which correspond to (TG)(N) conformations of the backbone, have a specific VROA backward signature in the form of an intense couplet around 1100 cm(-1). This couplet is associated with collective wagging and twisting motions, while most of its intensity comes from the anisotropic invariants combining normal coordinate derivatives of the electric dipole-electric dipole polarizability and of the electric dipole-magnetic dipole polarizability. A similar signature has already been found in model helical polyethylene chains, whereas it is very weak in forward VROA.

Proline Zwitterion Dynamics in Solution, Glass, and Crystalline State

Raman and Raman optical activity spectra of L- and D-proline zwitterionic (PROZW) forms were recorded for H(2)O and D(2)O solutions in a wide frequency range and analyzed with respect to the motion of the proline ring and rotation of the carbonyl group. The solution spectra were additionally compared to Raman scattering of glass and crystalline powder proline. Solution and glass spectral band broadenings are similar and reveal information about the extent of internal molecular motion. Two distinct but equally populated flexible forms were found in the glass and the solution. The equal population is consistent with NMR data, temperature, and concentration dependencies. The molecular flexibility is reduced significantly in the crystal, however, where only one conformer is present. Consequently, the crystal bands are narrow and exhibit minor frequency shifts. The spectra were interpreted with the aid of density functional theory computations involving both continuum and explicit solvent. A two-dimensional potential energy surface pertaining to the five-member ring puckering coordinates was constructed and used for dynamical averaging of spectral properties. Comparison of the computed and experimental bandwidths suggests that the puckering is strongly correlated with the carbonyl rotation. An averaging over these two motions produces similar results. The interpretation of the Raman experiments with the aid of the simulation techniques also indicates that the environment modulates properties of the hydrophobic part of the molecule indirectly by interacting with the ionic group. Such behavior may be important for the reactivity and biological activity of proline-containing peptides and proteins.