Density functional theory study of 1:1 glycine–water complexes in the gas phase and in solution

We present a systematic study of 1:1 glycine-water complexes involving all possible glycine conformers. The complex geometries are fully optimized for the first time both in the gas phase and in solution using three DFT methods (B3LYP, PBE1PBE, X3LYP) and the MP2 method. We calculate the G3 energies and use them as the reference data to gauge hydrogen bond strength in the gas phase. The solvent effects are treated via the integral equation formalism-polarizable continuum model (IEF-PCM). Altogether, we loca...     

A combined experimental inelastic neutron scattering, Raman and ab initio lattice dynamics study of α-lithium amidoborane

A combination of inelastic neutron scattering (INS) spectroscopy and Raman spectroscopy with periodic density functional theory calculations is used to provide a complete assignment of the vibrational spectra of α-lithium amidoborane (α-LiNH(2)BH(3)). The Born charge density and the atomic motion up to the decomposition temperature have been modelled. These models not only explain the nature of bonding in α-LiNH(2)BH(3) but also provide an insight into the atomic mechanisms of its decomposition. The (INS) measurements were performed in the range of 0-4000 cm(-1) on the high-resolution time-of-flight TOSCA INS spectrometer at the ISIS Spallation Neutron Source at the Rutherford Appleton Laboratory.     

Ab initio study of tautomerism and hydrogen bonding of β-carbonylamine in the gas phase and in water solution

All the possible conformations of the three tautomeric isomers of simple β-carbonylamine were fully optimized at ab initio MP2/6-31G** and B3LYP/6-31G** levels in order to determine the conformational equilibrium and the energies of the O—H···N and O···H—N hydrogen bridges. For the most interesting conformations, further calculations in water solution were also carried out. It was found that carbonylamine is the most stable tautomer, followed by enolimine and carbonylimine. This order of stability does not change in solution. O—H···N is the strongest hydrogen bridge, but in solution its energy as well as that of the O···H—N one are dramatically lowered. The deprotonation energy was also calculated and discussed. Received: 16 September 1999 / Accepted: 3 February 2000 / Published online: 5 June 2000     

N–H stretching frequencies and the conformation of substituted ureas: an ab initio MO study

The dependence of N–H stretching-mode frequencies in representative di- and trialkyl ureas on the conformational state of the ureido group has been studied by ab initio MO calculations using HF/3-21G and HF/6-31G** basis sets. The molecules studied were 1,3-dimethylurea, 1-methyl-3,3-dimethylurea and 1-methyl-3,3-di-iso-propylurea. The principal conclusions from the ab initio results are:

• 1.the trans–trans conformer (N–H bonds trans to the CO bond) has N–H stretching bands with about 20–30 cm⁻¹ higher frequency than the respective cis–cis structure, in accord with earlier literature assignments based on experimental data;
• 2.the N–H stretching frequency interval in tri-substituted ureas is 15–20 cm⁻¹ higher than the N–H band position in the 1,3-disubstituted molecule studied, the effect being determined mostly by the higher N–H stretching force constant;
• 3.in the absence of the steric hindrance the stable rotameric forms of the ureido grouping are almost planar at HF/3-21G level of calculations, while HF/6-31G** calculations predict a slightly pyramidal structure at the nitrogen atoms in the trans–trans conformer;
• 4.in 1-methyl-3,3-di-iso-propylurea the steric influence of the two bulky iso-propyl groups cause a deviation from planarity of the N–H bond. The non-planar conformation is accompanied by a shift of the N–H stretching mode frequency towards higher values; and
• 5.the variations of the theoretically estimated N–H stretching-mode frequencies appear to be principally determined by changes in the N–H stretching force constants in the different molecules.

© 1997 Elsevier Science B.V.     

The Jahn-Teller effect in CH3Cl+(X̃2E): a combined high-resolution experimental measurement and ab initio theoretical study

The energy levels of CH(3)Cl(+)X?(2)E showing strong spin-vibronic coupling effect (Jahn-Teller effect) have been measured up to 3500 cm(-1) above the ground vibrational state using one-photon zero-kinetic energy photoelectron and mass-analyzed threshold ionization spectroscopic method. Theoretical calculations have been also performed to calculate the spin-vibronic energy levels using a diabatic model and ab initio adiabatic potential energy surfaces (PESs). In the theoretical calculations the diabatic potential energy surfaces are expanded by the Taylor expansions up to the fourth-order including the multimode vibronic interactions. The calculated spin-orbit energy splitting (224.6 cm(-1)) for the ground vibrational state is in good agreement with the experimental data (219 ± 3 cm(-1)), which indicates that the Jahn-Teller and the spin-orbit coupling have been properly described in the theoretical model near the zero-point energy level. Based on the assignments predicted by the theoretical calculations, the experimentally measured energy levels were fitted to those from the diabatic model by optimizing the main spectroscopic parameters. The PESs from the ab initio calculations at the level of CASPT2/vq(t)z were thus compared with those calculated from the experimentally determined spectroscopic parameters. The theoretical diagonal elements in the diabatic potential matrix are in good agreement with those determined using the experimental data, however, the theoretical off-diagonal elements appreciably deviate from those determined using the experimental data for geometric points far away from the conical intersections. It is also concluded that the JT effect in CH(3)Cl(+) mainly arises from the linear coupling and the mode coupling between the CH(3) deform (υ(5)) and CH(3) rock (υ(6)) vibrations. The mode couplings between the symmetric C-Cl stretching vibration υ(3) with υ(5) and υ(6) are also important to understand the spin-vibronic structure of the molecule.     

Structures,g-tensors,and hyperfine coupling constants of L-α-alanine radicals in radiation dosimetry: An ab initio molecular dynamics simulation study

Alanine is used as a transfer standard dosimeter for gamma ray and electron beam calibration. An important factor affecting its dosimetric response is humidity which can lead to errors in absorbed dose calculations. Ab initio molecular dynamics calculations were performed to determine the environmental effects on the electron paramagnetic resonance (EPR) parameters of L-α-alanine radicals in acidic and alkaline solutions. A new result, not dissimilar to the closed-shell amino acid molecule alanine, is that the non-zwitterionic form of the alanine radical is the stable form in the gas phase while the zwitterionic neutral alanine radical is not a stable structure in the gas phase. Geometric and EPR parameters of radicals in both gas and solution phases are found to be dependent on hydrogen bonding of water molecules with the polar groups and on dynamic solvation. Calculations on the optimized free radicals in the gas phase revealed that for the neutral radical, hydrogen bonding to water molecules drives a decrease in the magnitudes of g-tensor components g _xx and g _yy without affecting neither g _zz component nor the hyperfine coupling constants (HFCCs). The transfer from the gas to solution phase of the alanine radical anion is accompanied with an increase in the spin density on the carboxylic group's oxygen atoms. However, for the neutral radical, this transfer from gas to solution phase is accompanied with the decrease in the spin density on oxygen atoms. Calculated isotropic HFCCs and g-tensor of all radicals are in good agreement with experiment in both acidic and alkaline solutions.     

Are the radical centers in peptide radical cations mobile? The generation, tautomerism, and dissociation of isomeric alpha-carbon-centered triglycine radical cations in the gas phase

The mobility of the radical center in three isomeric triglycine radical cations[G(*)GG](+), [GG(*)G](+), and [GGG(*)](+) has been investigated theoretically via density functional theory (DFT) and experimentally via tandem mass spectrometry. These radical cations were generated by collision-induced dissociations (CIDs) of Cu(II)-containing ternary complexes that contain the tripeptides YGG, GYG, and GGY, respectively (G and Y are the glycine and tyrosine residues, respectively). Dissociative electron transfer within the complexes led to observation of [Y(*)GG](+), [GY(*)G](+), and [GGY(*)](+); CID resulted in cleavage of the tyrosine side chain as p-quinomethide, yielding [G(*)GG](+), [GG(*)G](+), and [GGG(*)](+), respectively. Interconversions between these isomeric triglycine radical cations have relatively high barriers (> or = 44.7 kcal/mol), in support of the thesis that isomerically pure [G(*)GG](+), [GG(*)G](+), and [GGG(*)](+) can be experimentally produced. This is to be contrasted with barriers < 17 kcal/mol that were encountered in the tautomerism of protonated triglycine [Rodriquez C. F. et al. J. Am. Chem. Soc. 2001, 123, 3006-3012]. The CID spectra of [G(*)GG](+), [GG(*)G](+), and [GGG(*)](+) were substantially different, providing experimental proof that initially these ions have distinct structures. DFT calculations showed that direct dissociations are competitive with interconversions followed by dissociation.     

CHF3…H2O complex revisited: a matrix isolation and ab initio study

Structural Chemistry - The structural and spectroscopic features of the CHF3…H2O complex have been investigated using high-level ab initio calculations and IR matrix isolation spectroscopy....     

Application of deuterium–hydrogen exchange to study the secondary structure of oligonucleotide ions in a gas phase

At present, the secondary structure of oligonucleotide ions in a gas phase is almost not understood. One of the main points is the retention of a hairpin secondary structure during ionization. In this work, we used a deuterium–hydrogen exchange reaction in a gas phase at atmospheric pressure for studying the conformational dynamics of oligonucleotide ions formed as a result of electrospray ionization. The exchange reactions of two oligonucleotides, which consisted of the identical sets of nucleotides but differed in their sequence, have been studied. One of these oligonucleotides formed a hairpin secondary structure, but the other did not. It has been found that both of the oligonucleotides demonstrate similar reaction dynamics of deuterium/hydrogen exchange in the gas phase; thereby indicating that the secondary structure has been completely destroyed during ionization.     

Characterisation of H2S···CuCl and H2S···AgCl isolated in the gas phase: a rigidly pyramidal geometry at sulphur revealed by rotational spectroscopy and ab initio calculations

Pure rotational spectra of the ground vibrational states of eight isotopologues of H(2)S···CuCl and twelve isotopologues of H(2)S···AgCl have been analysed allowing rotational constants and hyperfine coupling constants to be determined. The molecular structures have been determined from the measured rotational constants and are presented alongside the results of calculations at the CCSD(T) level. Both molecules have C(s) symmetry at equilibrium and are pyramidal at the sulphur atom. The chlorine, metal, and sulphur atoms are collinear while the local C(2) axis of the hydrogen sulphide molecule intersects the axis defined by the heavy atoms at an angle, φ = 74.46(2)° for Cu and φ = 78.052(6)° for Ag. The molecular geometries are rationalised using simple rules that invoke the electrostatic interactions within the complexes. Centrifugal distortion constants, Δ(J), and nuclear quadrupole coupling constants, χ(aa)(Cu) and χ(aa)(Cl) for H(2)S···CuCl are presented for the first time. The geometry of H(2)S···AgCl is determined with fewer assumptions and greater precision than previously.     

An ab initio MO study on the direct and migratory reaction mechanism for the formation of HF in H+ClF system

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Perceiving molecular themes in the structures and bonding of intermetallic phases: the role of Hückel theory in an ab initio era

Qualitative molecular orbital theory is central to our understanding of the bonding and reactivity of molecules and materials across chemistry. Advances in computational technology and methodology, however, have made ab initio or density functional theory calculations a simpler alternative, offering reliable results on increasingly large systems in a reasonable time-scale without the need for concerns about the approximations and parameterization of semi-empirical one-electron based methods. In this perspective, we illustrate how the availability of higher-level computational results can augment, rather than supplant, the insights provided by approaches such as the simple and extended Hückel methods. We begin by describing a way to parameterize Hückel-type Hamiltonians against DFT results for intermetallic systems. The potential for chemical understanding embodied by such orbital-based models is then demonstrated with two schemes of bonding analysis that originated in them (but can be extended to DFT results): the μ(3)-acid/base model and the μ(2)-Hückel chemical pressure analysis, which translate the molecular concepts of acidity and electronic/steric competition, respectively, into the context of intermetallic chemistry.     

Car-Parinello molecular dynamics simulations of thionitroxide and S-nitrosothiol in the gas phase, methanol, and water—A theoretical study of S-nitrosylation

A dilemma about whether thionitroxide radical (RSNHO) or S-nitrosothiol (RSNO) is observed in protein S-nitrosylation has arisen recently. To illustrate the effect of chemical environment on these structures, this paper presents quantum mechanical molecular dynamics of thionitroxide, and cis-and trans-S-nitrosothiols in the gas phase, methanol, and water. By using Car-Parrinello molecular dynamics (CPMD), we have observed that there is free rotation about the S-N bond at 300 K in thionitroxide, but no such rotation is observed for S-nitrosothiol. The C-S-N-O torsion angle distribution in thionitroxide is s-ignificantly dependent upon the surrounding environment, leading to either gauche-, cis-, or trans-conformation. In the case of S-nitrosothiol the C-S-N-O plane is twisted slightly by 5°-15° in the cis-isomer, while the periplanar structure is well-retained in the trans-isomer. The calculated results are in agreement with the X-ray crystallographic data of small molecular RSNO species. Interestingly, for both compounds, the CPMD simulations show that solvation can cause a decrease in the S-N bond length. Moreover, the oxygen atom of thionitroxide is found to be a good hydrogen-bond acceptor, forming an oxyanion-hole-like hydrogen bonding network.     

Brønsted basicities of diamines in the gas phase, acetonitrile, and tetrahydrofuran

A comprehensive basicity study of alpha,omega-alkanediamines and related bases has been carried out. Basicities in acetonitrile (AN, pK(a) values), tetrahydrofuran (THF, pK(alpha) values), and gas phase (GP, GB values), were measured for 16, 14, and 9 diamine bases and for several related monoamines. In addition the gas-phase basicities and equilibrium geometries were computed for 19 diamino bases and several related monoamines at the DFT B3LYP 6-311+G** level. The effects of the different factors (intrinsic basicity of the amino groups, formation of intramolecular hydrogen bonds, and molecular strain) determining the diamine basicities were estimated by using the method of isodesmic reactions. The results are discussed in terms of molecular structure and solvation effects. The GP basicity is determined by the molecular size and polarizability, the extent of alkylation, and the energy effect of intramolecular hydrogen bond formation in the protonated base. The basicity trends in the solvents differ very much from those in GP: 1) The solvents severely compress the basicity range of the bases studied (3.5 times for the 1,3-propanediamine family in AN, and 7 times in THF), and 2) while stepwise alkylation of the basicity center leads to a steady basicity increase in the gas phase, the picture is complex in the solvents. Significant differences are also evident between THF and AN. The high hydrogen bond acceptor strength of THF leads to this solvent favoring the bases with "naked" protonation centers. In particular, the basicity order of N-methylated 1,3-propanediamines is practically inverse to that in the gas phase. The picture in AN is intermediate between that of GP and THF.     

Structural connectivity of 18-Crown-6/H+/L-tryptophan noncovalent complexes in gas phase and in solution: Delineating host–guest–solvent interactions in solution from gas phase structures

We investigate the structural correlation of noncovalent crown ether/H⁺/L-tryptophan (CR/TrpH⁺) host–guest complexes in the solution phase with those in the gas phase generated through electrospray ionization/mass spectrometry (ESI/MS) techniques. We perform quantum chemical calculations to determine their structures, relative Gibbs free energies, and infrared spectra. We compare the calculated infrared (IR) spectra with the IR multiphoton dissociation (IRMPD) spectra observed for the 18-Crown-6/TrpH⁺ complex by Polfer and co-workers [J. Phys. Chem. A 2013, 117, 1181–1188] for assigning the IR bands. We observe that the carboxyl group remains “naked,” lacking hydrogen bonding with the CR unit in the gas phase, and that this most stable conformer originates from the corresponding lowest Gibbs free energy structure in solution. Based on these findings, we propose that gas phase host–guest complexes directly correlate with those in solution, reinforcing the possibility of obtaining invaluable information about host–guest–solvent interactions in solution from the structure of the host–guest pair in the gas phase.     

Ab initio configuration interaction study of the structure and magnetic properties of radicals and radical ions derived from group 13–15 trihydrides

The structures, characteristic vibrations and magnetic properties of two isoelectronic series of radicals and radical ions derived from group 13–15 trihydrides have been investigated by post-Hartree-Fock theoretical techniques. Møller-Plesset perturbation theory based on an unrestricted Hartree-Fock determinant has been employed to determine the structures and vibrational frequencies in the 9-electron series, BH⁻₃, CH₃, and NH⁺₃. These species are found to be planar. Spin density distributions and ionization energetics have been estimated using a variational configuration interaction procedure. A positive electron affinity for BH₃ has not been demonstrated. The effect of out-of-plane vibrations on the hyperfine coupling constants is determined at a similar level of theory. In the 17-electron series AlH⁻₃, SiH₃, and PH⁺₃, pyramidal structures are found by using and extended split-valence basis at the SCF level. The computed harmonic force field suggests that a tentative assignment of a matrix isolated infrared spectrum to SiH₃ is incorrect. This conclusion is reinforced by calculation of the vibrational intensity patterns. Hyperfine interaction tensors computed at the optimized geometries from the UHF wavefunction with a more complete polarized double-zeta basis set are in accord with experiment. Vibrational effects are estimated by averaging the UHF spin density over an energy surface determined by second-order perturbation theory. Corrections due to vibrations are smaller than in the carbon series and single-point configuration interaction calculations confirm the reliability of the UHF spin densities.