Anharmonic Vibrational Spectroscopy of Nitriles and Their Complexes with Water

Insights into the molecular structure and infrared spectrum of the prebiotic species aminoacetonitrile

Aminoacetonitrile is an interstellar molecule with a prominent prebiotic role, already detected in the chemically-rich molecular cloud Sagittarius B2(N) and postulated to be present in the atmosphere of the largest Saturn's moon, Titan. To further support its observation in such remote environments and laboratory experiments aimed at improving our understanding of interstellar chemistry, we report a thorough spectroscopic and structural characterization of aminoacetonitrile. Equilibrium geometry, fundamental bands as well as spectroscopic and molecular parameters have been accurately computed by exploiting a composite scheme rooted in the coupled-cluster theory that accounts for the extrapolation to the complete basis set limit and core-correlation effects. In addition, a semi-experimental approach that combines ground-state rotational constants for different isotopic species and calculated vibrational corrections has been employed for the structure determination. From the experimental side, we report the analysis of the three strongest fundamental bands of aminoacetonitrile observed between 500 and 1000 cm^-1 in high-resolution infrared spectra. More generally, all computed band positions are in excellent agreement with the present and previous experiments. The only exception is the ν₁₅ band, for which we provide a revision of the experimental assignment, now in good agreement with theory.

Population Dynamics of Stretching Excitations of p-Azido-phenylalanine Incorporated in Calmodulin-Peptide Complexes

We genetically incorporated the unnatural amino acid p-azido-phenylalanine (AzF) into the ubiquitous Ca²⁺ sensor protein calmodulin (CaM) in complex with different peptides to explore the response of the azido stretching line shape to varying binding motifs with femtosecond infrared spectroscopy. The dynamic response of the azido stretching mode varies in different CaM-peptide complexes. We model these dynamics as coherent excitations of Fermi resonances and extract a lifetime of the azido stretching vibration of about 1 ps. The resulting model parameters are commensurate with the linear infrared absorption lineshapes which suggests that the conformation-sensitive vibrational lineshape could be composed of Fermi resonances that differ between the protein-peptide complexes.

Spectroscopy and second hyperpolarizability of odd spin states of acetonitrile: Theoretical study

The present study reports the spectroscopic characterization and second hyperpolarizability of odd spin states of acetonitrile in gas phase and water solvent. The odd spin states of acetonitrile are singlet, triplet and quintet spin state of acetonitrile have been considered for the study. The spectroscopic characterization viz. energy, geometrical parameters, infrared and electronic absorption spectra, molecular orbitals (MOs) their energies and natural transitions orbitals (NTOs) in gas phase and water solvent state reported at B3LYP/aug-cc-pVDZ level of theory. The second hyperpolarizability values are obtained using various methods and basis sets for comparison. It has been observed that the second hyperpolarizability values for the odd spin states of acetonitrile are more positive than the first hyperpolarizability. It is clearly seen that the effect of spin on spectroscopic parameters except on energy. The singlet gas phase acetonitrile calculations are well matching with the available experimental determinations. The TDDFT approach has been used to study electronic absorption spectra of all spin states of acetonitrile in gas phase and in water solvent. The IEFPCM model implemented in studying acetonitrile in water solvent at B3LYP/aug-cc-pVDZ level of theory. It is observed that HOMO to LUMO gap is larger for singlet than the triplet and quintet spin state and it decrease with an increase in strength of an applied field. All these calculations performed using Gaussian 16 program package.

Evidence and exploitation of dicationic ammonium-nitrilium superelectrophiles: direct synthesis of unsaturated piperidinones

Exploiting superacid activation, the reactivity of aminonitriles was enhanced through the transient formation of highly reactive ammonium-nitrilium superelectrophiles. Demonstrated by using in situ low-temperature NMR experiments and confirmed by X-ray diffraction analysis, these dications can be intramolecularly trapped by non-activated alkenes to generate unsaturated piperidinones, including enantioenriched ones, in a straightforward way.

Sensitivity of core-level spectroscopy to electrostatic environments of nitrile groups: An ab initio study

Ab initio quantum chemistry calculations have been performed to probe the influence of hydrogen bonding on the electronic structure of hydrogen cyanide (HCN). Our calculations determine the origin of nitrogen-specific Raman spectral features from resonant inelastic X-ray scattering occurring in the presence of a water molecule and an electric dipole field. The similarity of the two interactions in altering the electronic structure of the nitrogen atom differs only in the covalent contributions from the water molecule. The CN stretching mode as a structural probe was also investigated to study the electronic origin of the anomalous frequency shift of the nitrile group when subjected to hydrogen bonding and an electrostatic dipole field. The major changes in the electronic structure of HCN are electrostatic in nature and originate from dipole-dipole interactions. The relative shifts of the CN stretching frequency are in good agreement with those experimentally observed.

Electrostatic fields near the active site of human aldose reductase: 2. New inhibitors and complications caused by hydrogen bonds

Vibrational Stark effect spectroscopy was used to measure electrostatic fields in the hydrophobic region of the active site of human aldose reductase (hALR2). A new nitrile-containing inhibitor was designed and synthesized, and the X-ray structure of its complex, along with cofactor NADP(+), with wild-type hALR2 was determined at 1.3 Å resolution. The nitrile is found to be in the proximity of T113, consistent with a hydrogen bond interaction. Two vibrational absorption peaks were observed at room temperature in the nitrile region when the inhibitor binds to wild-type hALR2, indicating that the nitrile probe experiences two different microenvironments, and these could be empirically separated into a hydrogen-bonded and non-hydrogen-bonded population by comparison with the T113A mutant, in which a hydrogen bond to the nitrile is not present. Classical molecular dynamics simulations based on the structure predict a double-peak distribution in protein electric fields projected along the nitrile probe. The interpretation of these two peaks as a hydrogen bond formation-dissociation process between the probe nitrile group and a nearby amino acid side chain is used to explain the observation of two IR bands, and the simulations were used to investigate the molecular details of this conformational change. Hydrogen bonding complicates the simplest analysis of vibrational frequency shifts as being due solely to electrostatic interactions through the vibrational Stark effect, and the consequences of this complication are discussed.

Ni(+) reactions with aminoacetonitrile, a potential prebiological precursor of glycine

The gas-phase reactions between Ni(+) ((2)D(5/2)) and aminoacetonitrile, a molecule of prebiological interest as possible precursor of glycine, have been investigated by means of mass spectrometry techniques. The mass-analyzed ion kinetic energy (MIKE) spectrum reveals that the adduct ions [NC--CH(2)--NH(2), Ni(+)] spontaneously decompose by loosing HCN, H(2), and H(2)CNH, the loss of hydrogen cyanide being clearly dominant. The structures and bonding characteristics of the aminoacetonitrile-Ni(+) complexes as well as the different stationary points of the corresponding potential energy surface (PES) have been theoretically studied by density functional theory (DFT) calculations carried out at B3LYP/6-311G(d,p) level. A cyclic intermediate, in which Ni(+) is bisligated to the cyano and the amino group, plays an important role in the unimolecular reactivity of these ions, because it is the precursor for the observed losses of HCN and H(2)CNH. In all mechanisms associated with the loss of H(2), the metal acts as hydrogen carrier favoring the formation of the H(2) molecule. The estimated bond dissociation energy of aminoacetonitrile-Ni(+) complexes (291 kJ mol(-1)) is larger than those measured for other nitrogen bases such as pyridine or pyrimidine and only slightly smaller than that of adenine.

Efficient configuration selection scheme for vibrational second-order perturbation theory

A fast algorithm of vibrational second-order Moller-Plesset perturbation theory is proposed, enabling a substantial reduction in the number of vibrational self-consistent-field (VSCF) configurations that need to be summed in the calculations. Important configurations are identified a priori by assuming that a reference VSCF wave function is approximated well by harmonic oscillator wave functions and that fifth- and higher-order anharmonicities are negligible. The proposed scheme has reduced the number of VSCF configurations by more than 100 times for formaldehyde, ethylene, and furazan with an error in computed frequencies being not more than a few cm(-1).

Vibrational spectroscopic properties of hydrogen bonded acetonitrile studied by DFT

Vibrational properties (band position, Infrared and Raman intensities) of the acetonitrile C[triple bond]N stretching mode were studied in 27 gas-phase medium intensity (length range: = 1.71-2.05 angstroms; -deltaE range = 13-48 kJ/mol) hydrogen-bonded 1:1 complexes of CH3CN with organic and inorganic acids using density functional theory (DFT) calculations [B3LYP-6-31++G(2d,2p)]. Furthermore, general characteristics of the hydrogen bonds and vibrational changes in the OH stretching band of the acids were also considered. Experimentally observed blue-shifts of the C[triple bond]N stretching band promoted by the hydrogen bonding, which shortens the triple bond length, are very well reproduced and quantitatively depend on the hydrogen bond length. Both predicted enhancement of the infrared and Raman nu(C[triple bond]N) band intensities are in good agreement with the experimental results. Infrared band intensity increase is a direct function of the hydrogen bond energy. However, the predicted increase in the Raman band intensity increase is a more complex function, depending simultaneously on the characteristics of both the hydrogen bond (C[triple bond]N bond length) and the H-donating acid polarizability. Accounting for these two parameters, the calculated nu(C[triple bond]N) Raman intensities of the complexes are explained with a mean error of +/- 2.4%.

Differing Adsorption Behavior of Environmentally Important Cyanophenol Isomers at the Air−Water Interface

Vibrational sum-frequency spectroscopy and surface tensiometry have been used to study the adsorption of m- and p-cyanophenol at the air-water interface. Spectra of the cyano (CN) group under different polarization schemes are utilized to determine its hydrogen bonding environment and orientation. For both isomers, it is found that the cyano group is hydrogen bonded at the interface but that the CN orientation is independent of surface density. The average CN tilt angle (theta(0)), however, is found to differ between the isomers, such that the CN group points down toward the aqueous phase for m-cyanophenol (theta(0) = 96-106 degrees ) but points up toward the vapor phase for the p-cyanophenol (theta(0) = 65-80 degrees ). In addition, this average tilt angle is distributed over a narrow range, sigma(0) < 10 degrees for the meta isomer and sigma(0) < 16 degrees for the para isomer.

Simulation of photoelectron spectra with anharmonicity fully included: Application to the X̃A22←X̃A11 band of furan

Using a new unconventional procedure for calculating Franck-Condon factors with anharmonicity fully included the X 2A2<--X 1A1 band in the photoelectron spectrum of furan (and deuterated furan) was simulated at the second-order perturbation theory level. All 21 vibrational modes were considered but, in the end, only 4 are required to accurately reproduce the spectrum. Except for our own recent work on ethylene such calculations have been previously limited to tri- or tetraatomic molecules. Most of the effect of anharmonicity is accounted for in first order, although second-order corrections to the vibrational frequencies are important. Based on these simulations we were able to improve upon and extend previous assignments as well as suggest further measurements.

Highly accurate potential-energy and dipole moment surfaces for vibrational state calculations of methane

Full-dimensional ab initio potential-energy surface (PES) and dipole moment surface are constructed for a methane molecule at the CCSD(T)/cc-pVTZ and MP2/cc-pVTZ levels of theory, respectively, by the modified Shepard interpolation method based on the fourth-order Taylor expansion [MSI(4th)]. The reference points for the interpolation have been set in the coupling region of CH symmetric and antisymmetric stretching modes so as to reproduce the vibrational energy levels related to CH stretching vibrations. The vibrational configuration-interaction calculations have been performed to obtain the energy levels and the absorption intensities up to 9000 cm(-1) with the use of MSI(4th)-PES. The calculated fundamental frequencies and low-lying vibrational energy levels show that MSI(4th) is superior to the widely employed quartic force field, giving a better agreement with the experimental values. The absorption bands of overtones as well as combination bands, which are caused by purely anharmonic effects, have been obtained up to 9000 cm(-1). Strongly coupled states with visible intensity have been found in the 6500-9000 cm(-1) region where the experimental data are still lacking.

Pentachlorocyclopropane/Base Complexes: Matrix Isolation Infrared Spectroscopic and Density Functional Study of C−H- - -N Hydrogen Bonds

Hydrogen-bonded complexes of pentachlorocyclopropane with the bases acetonitrile, ammonia, monomethylamine, and dimethylamine have been isolated and characterized for the first time in argon matrices at 16 K. Coordination of the proton of pentachlorocyclopropane (Pccp) to the electron donor (N) of the base was evidenced by red shifts of the CH stretching mode. These shifts, which range from 22 to 170 cm(-1), increase in the order CH3CN, NH3, (CH3)NH2, and (CH3)2NH. Density functional theory (DFT) calculations at the B3LYP level agree well with experiment and support the formation of 1:1 complexes of Pccp/base. Distinct changes were observed in ring modes as well as CCl and CCl2 modes. The hydrogen bond energy of the complexes varies from 2.95 to 4.22 kcal/mol and is stronger than our previously studied bromocyclopropane-ammonia complex (2.35 kcal/mol, MP2).

Variational calculation of vibrational linear and nonlinear optical properties

A variational approach for reliably calculating vibrational linear and nonlinear optical properties of molecules with large electrical and/or mechanical anharmonicity is introduced. This approach utilizes a self-consistent solution of the vibrational Schrodinger equation for the complete field-dependent potential-energy surface and, then, adds higher-level vibrational correlation corrections as desired. An initial application is made to static properties for three molecules of widely varying anharmonicity using the lowest-level vibrational correlation treatment (i.e., vibrational Møller-Plesset perturbation theory). Our results indicate when the conventional Bishop-Kirtman perturbation method can be expected to break down and when high-level vibrational correlation methods are likely to be required. Future improvements and extensions are discussed.