Vibrational spectroscopy provides an important probe of the three-dimensional structures of peptides. With increasing size, these IR spectra become very complex and to extract structural information, comparison with theoretical spectra is essential. Harmonic DFT calculations have become a common workhorse for predicting vibrational frequencies of small neutral and ionized gaseous peptides. Although the far-IR region (<500 cm(-1)) may contain a wealth of structural information, as recognized in condensed phase studies, DFT often performs poorly in predicting the far-IR spectra of peptides. Here, Born-Oppenheimer molecular dynamics (BOMD) is applied to predict the far-IR signatures of two γ-turn peptides. Combining experiments and simulations, far-IR spectra can provide structural information on gas-phase peptides superior to that extracted from mid-IR and amide A features.

The structural organization of water at a model of amorphous silica-liquid water interface is investigated by ab initio molecular dynamics (AIMD) simulations at room temperature. The amorphous surface is constructed with isolated, H-bonded vicinal and geminal silanols. In the absence of water, the silanols have orientations that depend on the local surface topology (i.e. presence of concave and convex zones). However, in the presence of liquid water, only the strong inter-silanol H-bonds are maintained, whereas the weaker ones are replaced by H-bonds formed with interfacial water molecules. All silanols are found to act as H-bond donors to water. The vicinal silanols are simultaneously found to be H-bond acceptors from water. The geminal pairs are also characterized by the formation of water H-bonded rings, which could provide special pathways for proton transfer(s) at the interface. The first water layer above the surface is overall rather disordered, with three main domains of orientations of the water molecules. We discuss the similarities and differences in the structural organization of the interfacial water layer at the surface of the amorphous silica and at the surface of the crystalline (0 0 0 1) quartz surface.

Fructose has been examined under isolation conditions using a combination of UV ultrafast laser vaporization and Fourier-transform microwave (FT-MW) spectroscopy. The rotational spectra for the parent, all (six) monosubstituted (13)C species, and two single D species reveal unambiguously that the free hexoketose is conformationally locked in a single dominant β-pyranose structure. This six-membered-chair skeleton adopts a (2)C(5) configuration (equivalent to (1)C(4) in aldoses). The free-molecule structure sharply contrasts with the furanose form observed in biochemically relevant polysaccharides, like sucrose. The structure of free fructose has been determined experimentally using substitution and effective structures. The enhanced stability of the observed conformation is primarily attributed to a cooperative network of five intramolecular O-H···O hydrogen bonds and stabilization of both endo and exo anomeric effects. Breaking a single intramolecular hydrogen bond destabilizes the free molecule by more than 10 kJ mol(-1). The structural results are compared to ribose, recently examined with rotational resolution, where six different conformations coexist with similar conformational energies. In addition, several DFT and ab initio methods and basis sets are benchmarked with the experimental data.

Finite temperature Born-Oppenheimer DFT-based molecular dynamics simulations are presented for the vibrational spectroscopy of the prototype gas-phase Ala2H(+) and Ala3H(+) protonated peptides. The dynamics and the vibrational signatures are used to interpret IR-MPD spectra recorded in the NH/OH stretch region. Molecular dynamics simulations are one way to go beyond the harmonic approximations commonly applied for the calculations of infrared spectra, naturally including all anharmonicities, i.e. mode couplings, vibrational and dipole anharmonicities. The dynamics of the peptides allows understanding of the evolution of the shape and width of the N-H bands when increasing the size of the peptide, as demonstrated here with the two small prototypes Ala2H(+) and Ala3H(+). Hence, the conformational dynamics of Ala2(+) at room temperature participates to the broadening of the IR active bands. The complex N-H broadband of Ala3H(+) is shown to result from the dynamics of the N-H groups in the different peptide families, with a special role from breaking/reforming of hydrogen bonds involving the N-H groups. Taking this dynamics into account is thus mandatory for the understanding of this band in the 300-400 K experimental spectrum.

A theoretical study of C n Cl, C n Cl + , and C n Cl − (n = 1-7) clusters has been carried out. Predictions for their electronic structures, dipole moments, and vibrational frequencies have been made at the B3LYP/6-311G(d) level. According to our calculations the lowest-lying geometry of all these species (with the only exception of neutral C 3 Cl) is predicted to be either a linear or quasi-linear structure with chlorine located at the end of the carbon chain. C n Cl clusters all have doublet ground states, whereas the anionic clusters, with the only exception of CCl − , all have singlet ground states. For C n Cl + species, n-even clusters have triplet ground states whereas n-odd ones have singlet ground states. An even-odd parity effect (n-even clusters more stable than n-odd ones) is found for both the neutral and anionic species, whereas in the case of the cations the alternation in stability is reversed. The ionization potential (IP) and electron affinity (EA) also exhibit regular variations with the size of the cluster, with n-even clusters having both higher IP and EA than n-odd ones.

The local structure of phosphorylated residues in peptides and proteins may have a decisive role on their functional properties. Recent IRMPD experiments have started to provide spectroscopic signatures of such structural details; however, a proper modeling of these signatures beyond the harmonic approximation, taking into account temperature and entropic effects, is still lacking. In order to bridge this gap, DFT-based Car-Parrinello molecular dynamics simulations have been carried out for the first time on a phosphorylated amino acid, gaseous deprotonated phosphoserine. It is found that all vibrational signatures are successfully reproduced, and new deconvolution techniques enable the assignment of the vibrational spectrum directly from the dynamics results and the comparison of vibrational modes at several temperatures. The lowest energy structure is found to involve a strong hydrogen bond between the deprotonated phosphate and the acid with relatively small free energy barriers to proton transfer; however, we find that proton shuttling between the two sites does not occur frequently. Anharmonicities turn out to be important to reproduce the frequencies and shapes of several experimental bands. Comparison of room temperature and 13 K, effectively harmonic dynamics, allows insight to be obtained into vibrational anharmonicities. In particular, a significant blue-shift and broadening of the C═O stretching frequency from 13 to 300 K can be ascribed to intrinsic anharmonicity rather than to anharmonic coupling to other modes. On the other hand, significant couplings are found for the stretching motions of the hydrogen bonded P-O bond and of the free P-OH bond, mainly with modes within the phosphate group.

In this paper we report different theoretical approaches to study the gas-phase unimolecular dissociation of the doubly-charged cation [Ca(urea)](2+), in order to rationalize recent experimental findings. Quantum mechanical plus molecular mechanical (QM/MM) direct chemical dynamics simulations were used to investigate collision induced dissociation (CID) and rotational-vibrational energy transfer for Ar + [Ca(urea)](2+) collisions. For the picosecond time-domain of the simulations, both neutral loss and Coulomb explosion reactions were found and the differences in their mechanisms elucidated. The loss of neutral urea subsequent to collision with Ar occurs via a shattering mechanism, while the formation of two singly-charged cations follows statistical (or almost statistical) dynamics. Vibrational-rotational energy transfer efficiencies obtained for trajectories that do not dissociate during the trajectory integration were used in conjunction with RRKM rate constants to approximate dissociation pathways assuming complete intramolecular vibrational energy redistribution (IVR) and statistical dynamics. This statistical limit predicts, as expected, that at long time the most stable species on the potential energy surface (PES) dominate. These results, coupled with experimental CID from which both neutral loss and Coulomb explosion products were obtained, show that the gas phase dissociation of this ion occurs by multiple mechanisms leading to different products and that reactivity on the complicated PES is dynamically complex.

A theoretical study of the MgC n , MgC n + , and MgC n -(n ) 2-7) cyclic clusters has been carried out. Predictions for their electronic energies, rotational constants, dipole moments, and vibrational frequencies have been made at the B3LYP/6-311G(d) and B3LYP/6-311+G(d) levels. MgC n cyclic clusters generally have singlet ground states, whereas both cationic and anionic clusters have doublet ground states. An even-odd parity effect (n-even clusters being more stable than n-odd ones) is observed for both the neutral and anionic species, whereas in the case of the cations, there is no clear alternation in stability. Ionization potentials exhibit also a clear parity alternation trend, with n-even clusters having larger values than n-odd ones. In the case of electron affinities, initially the same behavior is observed, but for larger members the trend is reversed and n-odd compounds have higher electron affinity. It is also found that neutral clusters prefer cyclic structures over open-chain isomers, especially for high n. On the other hand open-chain ground states are predicted for both anionic and cationic clusters, except for the first members of the series.