Alvaro Cimas

Vibrational Spectra of Small Protonated Peptides from Finite Temperature MD Simulations and IRMPD Spectroscopy

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.

Free Fructose Is Conformationally Locked

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.

Six pyranoside forms of free 2-deoxy-D-ribose.

Carbohydrates are one of the most versatile biochemical building blocks, widely acting in energetic, structural, or recognition processes. The interpretation of the biological activity of saccharides is based on the structure and relative stability of their conformers. One of the obstacles to resolving the basic structure issues arises from their ability to form strong intermolecular hydrogen bonds with polar solvents, which in turn can result in conformational changes. A clear picture of the conformational panorama of isolated 2-deoxyd-ribose has been revealed using Fourier-transform microwave spectroscopy in conjunction with a UV ultrafast laser ablation source. Additionally, the availability of rotational data has been the main bottle-neck for examining the presence of these building blocks in interstellar space, so these studies could also be useful to the astrochemistry community. 2-Deoxy-d-ribose (2DR, C5H10O4; Figure 1a) is an important naturally occurring monosaccharide, present in nucleotides, which are the building blocks for DNA. In DNA, 2DR is present in the furanose (five-membered) ring form, whereas free in aqueous solution it cyclizes into fiveor six-membered rings, with the latter—the pyranoid form—being dominant. By closing the chain into a six-membered ring, the C1 carbon atom is converted into an asymmetric center, yielding two possible stereochemical a and b anomeric species (Figure 1b). In aqueous solution, 2DR primarily exists as a mixture of nearly equal amounts of a and b pyranose forms, present in their low-energy chair conformations, C1 and C4 (Figure 1c). [4] Such configurations are connected through ring inversion, thus establishing the axial or equatorial position of the OH group for each conformer. In addition, the monossacharides exhibit an unusual preferential stabilization of pyranose rings containing an axial OH group at the C1 carbon over the equatorial orientation, widely known as the anomeric effect, although its physical origin remains controversial. Nevertheless, structural analysis of 2DRmust take into consideration the intramolecular hydrogen bonding between adjacent OH groups. The formation of hydrogenbond networks reinforces their stability owing to hydrogenbond cooperativity effects. Such networks are fundamental to the molecular recognition of carbohydrates. By dissecting all these factors we can determine the most stable conformers of 2DR and the relative arrangement of the different hydroxy groups under isolated conditions, such as in the gas phase. In vacuo theoretical calculations, carried out on a-/bpyranoses, a-/b-furanoses, and open-chain conformations, predict 15 furanose and pyranose forms (Figure 1d, Table 1) in an energy window of 12 kJmol 1 above the predicted cc-apyr C1 global minimum. The notation used to label the different conformers include the symbols a and b to denote the anomer type, C1 and C4 to denote the pyranose chair form, C2-endo or C3-endo to denote the furanose envelope forms, and “c” or “cc” to indicate a clockwise or counterclockwise configuration of the adjacent OH bonds, respectively. A number is added to provide theMP2 energy ordering within the same family. To validate the predicted conformational behavior, comparison with precise experimental data of 2DR is needed. Previous experiments to determine the conformation of monosaccharides were based on X-ray and NMR measurements. However, these data are influenced by environmental effects associated with the solvent or crystal lattice. Recently, an IR spectrum of 2DR in an inert matrix in

The amorphous silica-liquid water interface studied by ab initio molecular dynamics (AIMD): local organization in global disorder

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 (0u20090u20090u20091) quartz surface.

Gas-Phase Peptide Structures Unraveled by Far-IR Spectroscopy: Combining IR-UV Ion-Dip Experiments with Born–Oppenheimer Molecular Dynamics Simulations†

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 (<500u2005cm(-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 amideu2005A features.

Collision induced dissociation of doubly-charged ions: Coulomb explosion vs. neutral loss in [Ca(urea)]2+ gas phase unimolecular reactivity via chemical dynamics simulations

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.

Proton transfer from the inactive gas-phase nicotine structure to the bioactive aqueous-phase structure.

The role of water in the structural change of nicotine from its inactive form in the gas phase to its bioactive form in aqueous solution has been investigated by two complementary theoretical approaches, i.e., geometry optimizations and molecular dynamics. Structures of the lowest-energy nicotineH(+)-(H(2)O)(n) complexes protonated either on the pyridine (inactive form) or pyrrolidine (active form) ring have been calculated, as well as the free-energy barriers for the proton-transfer tautomerization between the two cycles. These structures show chains of 2-4 water molecules bridging the two protonation sites. The room-temperature free-energy barrier to tautomerization along the minimum-energy path from the pyridine to the pyrrolidine cycle drops rapidly when the number of water molecules increases from 0 to 4, but still remains rather high (16 kJ/mol with four water molecules), indicating that the proton transfer is a rather difficult and rare event. We compare results obtained through this explicit water molecule approach to those obtained by means of continuum methods. Car-Parrinello molecular dynamics (CPMD) simulations of the proton-transfer process in bulk with explicit water molecules have been conducted at room temperature. No spontaneous proton transfers have been observed during the dynamics, and biased CPMD simulations have therefore been performed in order to measure the free-energy profile of the proton transfer in the aqueous phase and to reveal the proton-transfer mechanism through water bridges. The MD bias involves pulling the proton from the pyridine ring to the surrounding bulk. Dynamics show that this triggers the tautomerization toward the pyrrolidine ring, proceeding without energy barrier. The proton transfer is extremely fast, and protonation of the pyrrolidine ring was achieved within 0.5 ps. CPMD simulations confirmed the pivotal role played by the water molecules that bridge the two protonation sites of nicotine within the bulk of the surrounding water.

Experimental and Computational Thermodynamic Study of Three Monofluoronitrobenzene Isomers

The present work reports the thermodynamic study performed on three monofluorinated nitrobenzene derivatives by a combination of experimental techniques and computational approaches. The standard (p degrees = 0.1 MPa) molar enthalpies of formation in the liquid phase of the three isomers of fluoronitrobenzene were derived from the standard molar energies of combustion, in oxygen, at T = 298.15 K, measured by rotating bomb combustion calorimetry. The vapor pressure study of the referred compounds was done by a static method and, from the obtained results, the phase diagrams were elaborated, and the respective triple point coordinates, as well as the standard molar enthalpies of vaporization, sublimation and fusion, at T = 298.15 K, were determined. The combination of some of the referred thermodynamic parameters yielded the standard (p degrees = 0.1 MPa) molar enthalpies of formation in the gaseous phase, at T = 298.15 K, of the studied compounds: Delta(f)H(m)(o) (2-fluoronitrobenzene, g) = -(102.4 +/- 1.5) kJ x mol(-1), Delta(f)H(m)(o) (3-fluoronitrobenzene, g) = -(128.0 +/- 1.7) kJ x mol(-1), and Delta(f)H(m)(o) (4-fluoronitrobenzene, g) = -(133.9 +/- 1.4) kJ x mol(-1). Using the empirical scheme developed by Cox, values of standard molar enthalpies of formation in the gaseous phase were estimated and afterwards compared with the ones obtained experimentally, and both were interpreted in terms of the molecular structure of the compounds. The theoretically estimated gas-phase enthalpies of formation were calculated from high-level ab initio molecular orbital calculations at the G3(MP2)//B3LYP level of theory. The computed values compare very well with the experimental results obtained in this work and show that 4-fluoronitrobenzene is the most stable isomer from the thermodynamic point of view. Furthermore, this composite approach was also used to obtain information about the gas-phase basicities, proton and electron affinities and, finally, adiabatic ionization enthalpies.

Energetic study applied to the knowledge of the structural and electronic properties of monofluorobenzonitriles.

The present work reports an energetic and structural study of 2-fluoro-, 3-fluoro-, and 4-fluorobenzonitrile. The standard molar enthalpies of formation, in the condensed phase, of the three isomers were derived from the standard molar energies of combustion, in oxygen, at T = 298.15 K. The standard molar enthalpies of vaporization or sublimation (for 4-fluorobenzonitrile), at T = 298.15 K, were measured using high-temperature Calvet microcalorimetry. The combination of these two parameters yields the standard molar enthalpies of formation in the gaseous phase. The vapor-pressure study of the referred compounds was performed by a static method, and the enthalpies of phase transition derived from the application of the Clarke and Glew equation. Theoretically estimated gas-phase enthalpies of formation, basicities, proton and electron affinities, and adiabatic ionization enthalpies were calculated from the G3MP2B3 level of theory. In order to evaluate the electronic properties, the geometries were reoptimized at MP2/cc-pVTZ level, and the QTAIM and NICS were computed. On the basis of the donor-acceptor system, another approach for evaluating the electronic effect for these compounds, using the NBO is suggested. The UV-vis spectroscopy study for the three isomers was performed. The intensities and the band positions were correlated with the thermodynamic properties calculated computationally.

Thermochemistry of 2-methylbenzoxazole and 2,5-dimethylbenzoxazole: an experimental and computational study

The standard (p°xa0=xa00.1xa0MPa) molar energies of combustion of 2-methylbenzoxazole and 2,5-dimethylbenzoxazole were measured by static-bomb combustion calorimetry. The standard molar enthalpies of vapourization, at Txa0=xa0298.15xa0K, were obtained from high-temperature Calvet microcalorimetry. The experimental results enable the calculation of the standard molar enthalpies of formation in the gaseous state, at Txa0=xa0298.15xa0K, for both compounds, being the results discussed in terms of structural and energetic contributions. The theoretically estimated gas-phase enthalpies of formation were calculated from high-level ab initio molecular orbital calculations at the G3(MP2)//B3LYP level of theory. The computed values compare very well with the experimental results obtained in this work and show that the 2,5-dimethylbenzoxazole is enthalpically the most stable compound. Furthermore, this composite approach was also used to obtain information about the gas-phase basicities, proton and electron affinities and adiabatic ionization enthalpies.