Anharmonic vibrational properties by a fully automated second-order perturbative approach

Relative importance of first and second derivatives of nuclear magnetic resonance chemical shifts and spin-spin coupling constants for vibrational averaging

Relative importance of anharmonic corrections to molecular vibrational energies, nuclear magnetic resonance (NMR) chemical shifts, and J-coupling constants was assessed for a model set of methane derivatives, differently charged alanine forms, and sugar models. Molecular quartic force fields and NMR parameter derivatives were obtained quantum mechanically by a numerical differentiation. In most cases the harmonic vibrational function combined with the property second derivatives provided the largest correction of the equilibrium values, while anharmonic corrections (third and fourth energy derivatives) were found less important. The most computationally expensive off-diagonal quartic energy derivatives involving four different coordinates provided a negligible contribution. The vibrational corrections of NMR shifts were small and yielded a convincing improvement only for very accurate wave function calculations. For the indirect spin-spin coupling constants the averaging significantly improved already the equilibrium values obtained at the density functional theory level. Both first and complete second shielding derivatives were found important for the shift corrections, while for the J-coupling constants the vibrational parts were dominated by the diagonal second derivatives. The vibrational corrections were also applied to some isotopic effects, where the corrected values reasonably well reproduced the experiment, but only if a full second-order expansion of the NMR parameters was included. Contributions of individual vibrational modes for the averaging are discussed. Similar behavior was found for the methane derivatives, and for the larger and polar molecules. The vibrational averaging thus facilitates interpretation of previous experimental results and suggests that it can make future molecular structural studies more reliable. Because of the lengthy numerical differentiation required to compute the NMR parameter derivatives their analytical implementation in future quantum chemistry packages is desirable.

Experimental and ab-initio calculated vcd spectra of the first OH-stretching overtone of (1R)-(-) and (1S)-(+)-endo-BORNEOL

The near infrared (NIR) absorption and NIR-vibrational circular dichroism (NIR-VCD) spectra of dilute solutions of the two enantiomers of endo-borneol have been measured in the first OH-stretching overtone region (1600-1300 nm). By density functional theory (DFT) we calculate mechanical parameters, i.e. the harmonic mechanical frequency and the anharmonicity constant for the OH stretching, and anharmonic electrical parameters; i.e. the dependence on OH-bond length of atomic polar tensors and atomic axial tensors. We evaluate transition integrals for the calculations of rotational and dipole strengths by Morse anharmonic wavefunctions depending on mechanical harmonic frequencies and mechanical anharmonicity parameters that are calculated ab initio. Experimental and calculated spectra compare quite well and this fact allows us to associate differently signed NIR-VCD features with different conformational states of the OH-bond. Absorption features for the fundamental and for the second overtone of the OH stretching are also compared with experiment.

H2CO3(s): a new candidate for CO2 capture and sequestration

To reduce the magnitude of anthropogenic global warming it is necessary to remove CO2(g) from the effluent streams of coal-fired power plants and to sequester the CO2 either as a liquid or by reaction with other compounds. A major difficulty in achieving this goal arises from the very weak acidity of CO2(g), causing it to react only incompletely with weak bases, although this weak interaction does provide a means for "stripping" the CO2 from the acid-base complex at high temperatures. Reaction with strong bases like Na0H yields more stable complexes, but massive amounts of chemical reactants would need to be purchased and chemical products like NaHCO3 then stored. However, when gas-phase CO2 reacts with the weak base water (or when bicarbonate reacts with strong acid) the unstable product monomeric "H2CO3" can be formed. The free energy required is about 16 kcal/mol in the gas phase and about 10 kcal/mol in aqueous solution. This energy can be supplied by particle or photon excitation and is only a small fraction ofthe energy released when a mole of CH4 is converted to a mole of CO2. Although this monomeric compound is highly unstable, its oligomers are considerably more stable, due to internal H-bonding, with free energies for the larger oligomers in the gas phase which are about 4 kcal/(mol of H2CO3) lower, only about 6 kcal/mol H2CO3 higher than the gas-phase combination of CO2 and H2O at room temperature. Also, at lower temperature the entropic penalty for the oligomer is less and oligomeric H2CO3 becomes stable around the sublimation temperature of dry ice. This indicates that it may be possible to capture gas-phase CO2 directly, using only cheap and abundant H2O as a reactant, and to store the resulting (H2CO3)n as a oligomeric solid at only moderately cold temperatures. These conclusions are based on quantum computations that accurately reproduce the structures, spectra, and stabilities of H2CO3 oligomers. Methods for producing and characterizing the H2CO3 oligomers are discussed. However, some aspects of the proposed scheme are quite speculative and will require additional investigation. Several important questions need to be answered before the feasibility of this procedure on a planetary scale can be assessed, particularly those involving the vapor pressure curve, heat of sublimation, density, and compressibility of (H2CO3)n.

Alanine polypeptide structural fingerprints at room temperature: what can be gained from non-harmonic Car-Parrinello molecular dynamics simulations

Structural infrared fingerprints of neutral gas phase alanine peptides of increasing size and complexity (dipeptide, octapeptide, and beta-strand peptide) are characterized through DFT-based Car-Parrinello molecular dynamics simulations. Harmonic and nonharmonic vibrational signatures are calculated from the time correlation of the dipole moment of the gas phase peptide in a direct way (without any approximation) respectively from low temperature (20 K) and room temperature (300 K) molecular dynamics. Our main purpose is to answer the two following questions: (i) Is the direct inclusion of temperature for the calculation of infrared spectra mandatory for the comprehension of the vibrational signatures experimentally recorded at room temperature? (ii) To what extent is the amide I, II, and III domain sensitive enough to the local structure of the peptides, to provide vibrational signatures that can be definitely used to assess the peptide conformation at 300 K?

Fully Integrated Approach to Compute Vibrationally Resolved Optical Spectra: From Small Molecules to Macrosystems

A general and effective time-independent approach to compute vibrationally resolved electronic spectra from first principles has been integrated into the Gaussian computational chemistry package. This computational tool offers a simple and easy-to-use way to compute theoretical spectra starting from geometry optimization and frequency calculations for each electronic state. It is shown that in such a way it is straightforward to combine calculation of Franck-Condon integrals with any electronic computational model. The given examples illustrate the calculation of absorption and emission spectra, all in the UV-vis region, of various systems from small molecules to large ones, in gas as well as in condensed phases. The computational models applied range from fully quantum mechanical descriptions to discrete/continuum quantum mechanical/molecular mechanical/polarizable continuum models.

Anomalously strong effect of the ion sign on the thermochemistry of hydrogen bonded aqueous clusters of identical chemical composition

The sign preference of hydrogen bonded aqueous ionic clusters X±(H₂O)_i (n =1–5, X = F; Cl; Br) has been investigated using the Density Functional Theory and ab initio MP2 method. The present study indicates the anomalously large difference in formation free energies between cations and anions of identical chemical composition. The effect of vibrational anharmonicity on stepwise Gibbs free energy changes has been investigated, and possible uncertainties associated with the harmonic treatment of vibrational spectra have been discussed.

What makes the huge 31P-31P coupling constants in S(PF2)2 and Se(PF2)2 vary so much with temperature?

The enormous temperature dependence of the (2)J(PP) coupling constants in S(PF(2))(2) and Se(PF(2))(2) has been explained by a theoretical investigation of their conformations and NMR coupling constants. In contrast, the coupling in O(PF(2))(2) is almost invariant. Gas electron diffraction data for S(PF(2))(2) have been reinterpreted. The results show that two conformers, with C(s) and C(2v) symmetry, exist for the S and Se compounds. The C(s) and C(2v) conformers have very different (2)J(PP) coupling constants (-12.6 and 395.2 Hz for S(PF(2))(2) at B3LYP/aug-cc-pVQZ) and thermal interconversion of these conformers explains the experimental behavior.

Toward spectroscopic accuracy for organic free radicals: Molecular structure, vibrational spectrum, and magnetic properties of F(2)NO

The structure, harmonic frequencies, and hyperfine couplings of F(2)NO have been computed by the coupled cluster ansatz using a hierarchical series of basis sets and, in some cases, extrapolation procedures to reach the complete basis set limit. Methods rooted into the density functional theory have been used to estimate anharmonic and environmental effects. The remarkable agreement with experimental hyperfine coupling constants and most of vibrational frequencies confirms the reliability of the computational approach and suggests that one of the observed frequencies probably refers to a different species.

Assessment of a computational strategy approaching spectroscopic accuracy for structure, magnetic properties and vibrational frequencies of organic free radicals: the F(2)CN and F(2)BO case

The molecular structure, vibrational frequencies, and hyperfine couplings of F(2)CN and F(2)BO have been computed at the coupled cluster level in conjunction with hierarchical series of correlation consistent basis sets. For geometrical and hyperfine parameters, extrapolation to the complete basis set limit and inclusion of core correlation effects have been considered. While a remarkable agreement with most of vibrational frequencies supports the reliability of the computational approach followed, experimental geometries cannot be used for validation purposes due to their limited accuracy. In view of previous experience with related radicals, the computed hyperfine coupling constants as well as molecular structures are expected to be very reliable and accurate.

Integrated computational approach to vibrationally resolved electronic spectra: anisole as a test case

A new general and effective procedure to compute Franck-Condon spectra from first principles is exploited to elucidate the subtle features of the vibrationally resolved optical spectra of anisole. Methods based on the density functional theory and its time-dependent extension for electronic excited states [B3LYP6-311+G(d,p) and TD-B3LYP6-311+G(d,p)] have been applied to geometry optimizations and harmonic frequency calculations. Perturbative anharmonic frequencies [J. Chem. Phys. 122, 014108 (2005)] have been calculated for the ground state, and the Duschinsky matrix elements have been used to evaluate the corresponding anharmonic corrections for the first excited electronic state. The relative energetics of both electronic states has been refined by single point calculations at the coupled clusters (CC) level with the aug-cc-pVDZ basis set. Theoretical spectra have been evaluated using a new optimized implementation for the effective computation of Franck-Condon factors. The remarkable agreement between theoretical and experimental spectra allowed for revision of some assignments of fundamental vibrations in the S(1) state of anisole.

Molecular structure of the octatetranyl anion, C8H-: a computational study

The equilibrium molecular structure of the octatetranyl anion, C8H(-), which has been recently detected in two astronomical environments, is investigated with the aid of both ab initio post-Hartree-Fock and density functional theory (DFT) calculations. The model chemistry adopted in this study was selected after a series of benchmark calculations performed on molecular acetylene for which accurate gas-phase structural data are available. Geometry optimizations performed at the CCSD/6-311+G(2d,p), QCISD/6-311+G(2d,p), and MP4(SDQ)/6-311+G(2d,p) levels of theory yield for C8H(-) an interesting polyyne-type structure that defies the chemical formula displaying a simple alternation of triple and single carbon-carbon bonds, [:C[triple bond]C-C[triple bond]C-C[triple bond]C-C[triple bond]CH](1-). In the optimized geometry of C8H(-), as one proceeds from the naked carbon atom on one side of the chain to the CH unit on the opposite side of the chain, the short (formally triple) carbon-carbon bonds decrease in length from 1.255 to 1.213 A whereas the long (formally single) carbon-carbon bonds increase (albeit only slightly) in length from 1.362 to 1.378 A (CCSD results). In striking contrast, both MP2 and DFT (B3LYP and PBE0) calculations fail in reproducing the pattern of the carbon-carbon bond lengths obtained with the CCSD, QCISD, and MP4 methods. The structures of three shorter n-even chains, C(n)H(-) (n = 2, 4, and 6), along with those of four n-odd compounds (n = 3, 5, 7, and 9) are also investigated at the CCSD/6-311+G(2d,p) level of theory.

Intermolecular HH vibrations of dihydrogen bonded complexes H3EH(-)...HOR in the low-frequency region: theory and IR spectra

The results of DFT calculations of harmonic and anharmonic frequencies of the dihydrogen bonded (DHB) complexes H 3EH (-)...HOR (E = B, Al, Ga and HOR = CH 3OH, CF 3CH 2OH) in gas phase and in low polar medium (by CPCM model) in comparison with the partners are presented. Normal coordinate analysis of the low-frequency modes was carried out to assign the new vibrations induced by DHB formation by the potential energy distribution values. Among them, the intermolecular H...H stretching vibrations only have individual modes. The influence of central atom mass and isotope and the strength of the proton donor effects were determined. The systems convenient for IR studies were chosen from the calculation predictions. The spectral investigation was made on the BH 4 (-)/ROH complexes (ROH = CH 2FCH 2OH (MFE), CF 3CH 2OH (TFE), (CF 3) 2CHOH (HFIP)). The results of temperature dependence, isotope substitution, and influence of the proton-donor strength studies agree with the theoretical conclusions. Combination of experimental and theoretical approaches allowed determining for the first time the intermolecular stretching mode characterizing intrinsic DHB vibrations.

Quantum mechanical computations and spectroscopy: from small rigid molecules in the gas phase to large flexible molecules in solution

Interpretation of structural properties and dynamic behavior of molecules in solution is of fundamental importance to understand their stability, chemical reactivity, and catalytic action. While information can be gained, in principle, by a variety of spectroscopic techniques, the interpretation of the rich indirect information that can be inferred from the analysis of experimental spectra is seldom straightforward because of the subtle interplay of several different effects, whose specific role is not easy to separate and evaluate. In such a complex scenario, theoretical studies can be very helpful at two different levels: (i) supporting and complementing experimental results to determine the structure of the target molecule starting from its spectral properties; (ii) dissecting and evaluating the role of different effects in determining the observed spectroscopic properties. This is the reason why computational spectroscopy is rapidly evolving from a highly specialized research field into a versatile and widespread tool for the assignment of experimental spectra and their interpretation in terms of chemical physical effects. In such a situation, it becomes important that both computationally and experimentally oriented chemists are aware that new methodological advances and integrated computational strategies are available, providing reliable estimates of fundamental spectral parameters not only for relatively small molecules in the gas phase but also for large and flexible molecules in condensed phases. In this Account, we review the most significant methodological contributions from our research group in this field, and by exploiting some recent results of their application to the computation of IR, UV-vis, NMR, and EPR spectral parameters, we discuss the microscopic mechanisms underlying solvent and vibrational effects on the spectral parameters. After reporting some recent achievements for the study of excited states by first principle quantum mechanical approaches, we focus on the treatment of environmental effects by means of mixed discrete-continuum solvent models and on effective methods for computing vibronic contributions to the spectra. We then discuss some new developments, mainly based on time-dependent approaches, allowing us to go beyond the determination of spectroscopic parameters toward the simulation of line widths and shapes. Although further developments are surely needed to improve the accuracy and effectiveness of several items in the proposed approach, we try to show that the first important steps toward a direct comparison between the results obtained in vitro and those obtained in silico have been made, making easier fruitful crossovers among experiments, computations and theoretical models, which would be decisive for a deeper understanding of the spectral behavior associated with complex systems and processes.

Determining transition-state geometries in liquids using 2D-IR

Many properties of chemical reactions are determined by the transition state connecting reactant and product, yet it is difficult to directly obtain any information about these short-lived structures in liquids. We show that two-dimensional infrared (2D-IR) spectroscopy can provide direct information about transition states by tracking the transformation of vibrational modes as a molecule crossed a transition state. We successfully monitored a simple chemical reaction, the fluxional rearrangement of Fe(CO)5, in which the exchange of axial and equatorial CO ligands causes an exchange of vibrational energy between the normal modes of the molecule. This energy transfer provides direct evidence regarding the time scale, transition state, and mechanism of the reaction.