Vibrational zero-point energies and thermodynamic functions beyond the harmonic approximation

Investigations of an O-H...S hydrogen bond via Car-Parrinello and path integral molecular dynamics

The presence of intramolecular hydrogen bonds influences the binding energy, tautomeric equilibrium, and spectroscopic properties of various classes of organic molecules. This article discusses the O-H...S bridge, one of the less commonly investigated types of intramolecular interactions. 3-mercapto-1,3-diphenylprop-2-en-1-one was considered as the model structure. This compound exhibits photochromic properties. Car-Parrinello molecular dynamics (CPMD) was applied to investigate the spectroscopic and molecular properties of this compound in the gas phase and in the solid state. The second part of the study is devoted to the effects of the quantization of nuclear motions, with special attention to the O-H...S moiety. Path integral molecular dynamics (PIMD) of the molecular crystal of 3-mercapto-1,3-diphenylprop-2-en-1-one was carried out for this purpose. The employment of this fully quantum mechanical technique enables one to study, in a time-averaged sense, the zero-point motion important for flat potential energy surfaces. Finally, the potentials of mean force (Pmfs) were calculated from the CPMD and PIMD data obtained for the solid-state calculations. The effect of including quantum nuclear motion was investigated. In the studied compound, quantum effects shortened the H-bridge and provided a better description of the free energy minimum. The computational results place this uncommon intramolecular H-bonding among the class of strong hydrogen bonds with large red shifts of O-H stretching modes, which correspond well with previously presented experimental data in the literature concerning this structure.

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.

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.

Calculated spectroscopic and electric properties of the alkali metal-ammonia complexes from Kn–NH3 to Frn–NH3 (n=0,+1)

The newly developed Stuttgart small-core scalar relativistic pseudopotentials for the alkali metals are used to study spectroscopic and electric properties of the heavier alkali metal-ammonia complexes from K(n)-NH(3) to Fr(n)-NH(3) (n=0,+1) at the second-order Moller-Plesset (MP2) and coupled cluster [CCSD(T)] levels of theory. Equilibrium geometries and dissociation energies computed at the MP2 level are in reasonable agreement with their CCSD(T) counterparts, whereas for the dipole polarizabilities MP2 is not performing well overestimating significantly electron correlation effects. The bond distances increase monotonically with increasing mass of the metal atom as relativistic effects are small in these systems. However, the dipole polarizabilities are more sensitive to such effects and we find a decrease in this property from Cs-NH(3) to Fr-NH(3). Combination of CCSD(T) harmonic frequencies and MP2 anharmonic corrections obtained from a perturbative vibrational treatment leads to fundamental frequencies in good agreement with experimental results obtained by Suzer and Andrews [J. Am. Chem. Soc. 109, 300 (1986)]. We also present the results of variational calculations with a three-dimensional vibrational Hamiltonian, making use of CCSD(T) potential energy and electric dipole moment surfaces. Complexation of NH(3) to the metal causes a strong infrared intensification of the symmetric NH(3) stretching mode in the neutral complexes, which is absent in the charged species.

Signature of the Conformational Preferences of Small Peptides: a Theoretical Investigation

An extensive computational study of the conformational preferences of N-acetylphenylalaninylamide (NAPA) is reported, including conformational and anharmonic frequency analyses, as well as calculations of excitation energies of the four NAPA conformers lowest in energy. Particular attention is paid to the influence of hydrogen-bonding interactions on the relative stability of the conformers, which was found to be very sensitive to both the level of quantum chemical computations and the anharmonic treatment of molecular vibrations. The assignments of the UV spectral peaks are well supported by the multireference CASSCF/MS-CASPT2 calculations. Upon consideration of the second-order Möller-Plesset (MP2) and density functional theory (DFT) structures, overall energetics, and harmonic and anharmonic corrections, we found no conclusive theoretical evidence for the assumed conformational propensity of small model peptides toward extended beta-strand structures.

Study of NH Stretching Vibrations in Small Ammonia Clusters by Infrared Spectroscopy in He Droplets and ab Initio Calculations†

Infrared spectra of the NH stretching vibrations of (NH3)n clusters (n = 2-4) have been obtained using the helium droplet isolation technique and first principles electronic structure anharmonic calculations. The measured spectra exhibit well-resolved bands, which have been assigned to the nu1, nu3, and 2nu4 modes of the ammonia fragments in the clusters. The formation of a hydrogen bond in ammonia dimers leads to an increase of the infrared intensity by about a factor of 4. In the larger clusters the infrared intensity per hydrogen bond is close to that found in dimers and approaches the value in the NH3 crystal. The intensity of the 2nu4 overtone band in the trimer and tetramer increases by a factor of 10 relative to that in the monomer and dimer, and is comparable to the intensity of the nu1 and nu3 fundamental bands in larger clusters. This indicates the onset of the strong anharmonic coupling of the 2nu4 and nu1 modes in larger clusters. The experimental assignments are compared to the ones obtained from first principles electronic structure anharmonic calculations for the dimer and trimer clusters. The anharmonic calculations were performed at the Møller-Plesset (MP2) level of electronic structure theory and were based on a second-order perturbative evaluation of rovibrational parameters and their effects on the vibrational spectra and average structures. In general, there is excellent (<20 cm(-1)) agreement between the experimentally measured band origins for the N-H stretching frequencies and the calculated anharmonic vibrational frequencies. However, the calculations were found to overestimate the infrared intensities in clusters by about a factor of 4.

Interplay of Intrinsic, Environmental, and Dynamic Effects in Tuning the EPR Parameters of Nitroxides: Further Insights from an Integrated Computational Approach

The role of stereoelectronic, environmental, and short-time dynamic effects in tuning the hyperfine and gyromagnetic tensors of a prototypical nitroxide spin probe has been investigated by an integrated computational approach based on extended Lagrangian molecular dynamics and discrete-continuum solvent models. Trajectories were generated in two protic solvents as well as in the gas phase for reference; structural analysis of the dynamics, and comparison with optimized solute-solvent clusters, allowed for the identification of the prevailing solute-solvent hydrogen-bonding patterns and helped to define the strategy for the computation of magnetic parameters. This was performed in a separate step, on a large number of frames, by a high-level DFT approach coupling the PBE0 hybrid functional with a tailored basis set and with proper account of specific and bulk solvent effects. Remarkable changes in solvation networks are found on going from aqueous to methanol solution, thus providing a rationalization of indirect experimentally available evidence. The computed magnetic parameters are in satisfactory agreement with the available measured values and allow for an unbiased evaluation of the role of different effects in tuning the overall EPR observables. Apart from their intrinsic interest, our results pave the route toward the development of tunable detection protocols based on specific spectroscopic signatures.

Concerted and Stepwise Reaction Mechanisms for the Addition of Ozone to Acetylene: A Computational Study

The mechanism of the reaction between acetylene and ozone to form a primary ozonide (POZ) in the gas phase has been studied theoretically. The concerted pathway, HCCH + O3 --> POZ, proceeds via a biradicaloid transition state TS0. The stepwise pathway is a three-step reaction, HCCH + O3 --> M1 --> M2 --> POZ, involving two biradical TSs and two biradical intermediates M1 and M2. The segment of the global potential energy surface (PES) for the concerted pathway is characterized as a R-PES, which is obtained from the restricted (R) density functional theory and Hartree-Fock-based methods. The RDFT and RHF solutions of TS0 and O3 are unstable toward spin-symmetry breaking. The wave function instability for TS0 and O3 results in a discontinuity between the R-PES and the region of the global PES encompassing the biradical TSs and the intermediates of the stepwise pathway, which are characterized with unrestricted (U) methods. The global PES is characterized separately as an U(R)-PES using a combination of the R and U methods. Several different values of barriers for the concerted pathway and the energy of concert (Ec) can be estimated due to complications arising from the discontinuity between the R- and the U(R)-PES and the existence of two different RDFT and UDFT O3 equilibrium geometries. RCCSD(T)//RDFT predicts a barrier of 8.2 kcal/mol. U(R)CCSD(T)/U(R)DFT predicts a barrier of 13.8 kcal/mol for the concerted and 15.3 kcal/mol for the stepwise pathway. Comparison between the R-PES barrier to the concerted pathway and the U(R)-PES barrier to the stepwise pathway suggests the former to be the only significant mechanism. Consideration of the energy difference between TS1, the TS for the first step of the stepwise mechanism, and TS0 within the global PES leads to a significantly smaller Ec. Geometry optimization with CASSCF and energy point calculations with MRMP2 are employed to characterize TS0 and TS1. MRMP2//CASSCF predicts the energy level of TS1 to be higher than that of TS0 by 2 kcal/mol. Analysis of experimental and computational data based on the low estimate of Ec shows that the possibility of the stepwise pathway being a secondary channel at elevated temperatures cannot be ruled out.

Combined vacuum ultraviolet laser and synchrotron pulsed field ionization study of CH2BrCl

The pulsed field ionization-photoelectron (PFI-PE) spectrum of bromochloromethane (CH2BrCl) in the region of 85,320-88,200 cm-1 has been measured using vacuum ultraviolet laser. The vibrational structure resolved in the PFI-PE spectrum was assigned based on ab initio quantum chemical calculations and Franck-Condon factor predictions. At energies 0-1400 cm-1 above the adiabatic ionization energy (IE) of CH2BrCl, the Br-C-Cl bending vibration progression (nu1+=0-8) of CH2BrCl+ is well resolved and constitutes the major structure in the PFI-PE spectrum, whereas the spectrum at energies 1400-2600 cm-1 above the IE(CH2BrCl) is found to exhibit complex vibrational features, suggesting perturbation by the low lying excited CH2BrCl+(A 2A") state. The assignment of the PFI-PE vibrational bands gives the IE(CH2BrCl)=85,612.4+/-2.0 cm-1 (10.6146+/-0.0003 eV) and the bending frequencies nu1+(a1')=209.7+/-2.0 cm-1 for CH2BrCl+(X2A'). We have also examined the dissociative photoionization process, CH2BrCl+hnu-->CH2Cl++Br+e-, in the energy range of 11.36-11.57 eV using the synchrotron based PFI-PE-photoion coincidence method, yielding the 0 K threshold or appearance energy AE(CH2Cl+)=11.509+/-0.002 eV. Combining the 0 K AE(CH2Cl+) and IE(CH2BrCl) values obtained in this study, together with the known IE(CH2Cl), we have determined the 0 K bond dissociation energies (D0) for CH2Cl+-Br (0.894+/-0.002 eV) and CH2Cl-Br (2.76+/-0.01 eV). We have also performed CCSD(T, full)/complete basis set (CBS) calculations with high-level corrections for the predictions of the IE(CH2BrCl), AE(CH2Cl+), IE(CH2Cl), D0(CH2Cl+-Br), and D0(CH2Cl-Br). The comparison between the theoretical predictions and experimental determinations indicates that the CCSD(T, full)/CBS calculations with high-level corrections are highly reliable with estimated error limits of <17 meV.

Theoretical Prediction and the First IR Matrix Observation of SeveralL-Cysteine Molecule Conformers

For the first time the argon-matrix low-temperature IR spectra of cysteine are recorded. They reveal a quite complicated spectral pattern, which can also be reproduced in the N2 matrix. Assignment of the observed spectra is undertaken on the basis of comparison of the experimental and calculated B3LYP/aug-cc-pVDZ anharmonic IR spectra. The presence of at least three, and possibly even six or more, cysteine conformers with and without intramolecular hydrogen bonding is confirmed. On the basis of the calculated vibrational circular dichroism spectra, we predict this technique to be more distinctive for conformers than IR absorption is.

Infrared photodissociation of a water molecule from a flexible molecule-H2O complex: Rates and conformational product yields following XH stretch excitation

Infrared-ultraviolet hole-burning and hole-filling spectroscopies have been used to study IR-induced dissociation of the tryptamine.H2O and tryptamine.D2O complexes. Upon complexation of a single water molecule, the seven conformational isomers of tryptamine collapse to a single structure that retains the same ethylamine side chain conformation present in the most highly populated conformer of tryptamine monomer. Infrared excitation of the tryptamine.H2O complex was carried out using a series of infrared absorptions spanning the range of 2470-3715 cm-1. The authors have determined the conformational product yield over this range and the dissociation rate near threshold, where it is slow enough to be measured by our methods. The observed threshold for dissociation occurred at 2872 cm-1 in tryptamine.H2O and at 2869 cm-1 in tryptamine.D2O, with no dissociation occurring on the time scale of the experiment (approximately 2 micros) at 2745 cm-1. The dissociation time constants varied from approximately 200 ns for the 2869 cm-1 band of tryptamine.D2O to approximately 25 ns for the 2872 cm-1 band of tryptamine.H2O. This large isotope dependence is associated with a zero-point energy effect that increases the binding energy of the deuterated complex by approximately 190 cm-1, thereby reducing the excess energy available at the same excitation energy. At all higher energies, the dissociation lifetime was shorter than the pulse duration of our lasers (8 ns). At all wavelengths, the observed products in the presence of collisions are dominated by conformers A and B of tryptamine monomer, with small contributions from the other minor conformers. In addition, right at threshold (2869 cm-1), tryptamine.D2O dissociates exclusively to conformer A in the absence of collisions with helium, while both A and B conformational products are observed in the presence of collisions with helium. Using resolution-of-identity approximation to second-order Moller-Plesset binding energies extrapolated to the complete basis set limit and harmonic vibrational frequencies and transition states calculated at the density functional limit B3LYP/6-31+G* level of theory, Rice-Ramsperger-Kassel-Marcus (RRKM) predictions for the dissociation, isomerization, and water shuttling rates as a function of energy are made. At threshold, the experimental dissociation rate is almost 10(3) faster than RRKM predictions. Reasons for this apparent non-RRKM behavior will be discussed.