Analysis of vibrational spectra of L-alanylglycine based on density functional theory calculations

FT Raman and IR spectra of the crystallized biologically active molecule, L-alanylglycine (L-Ala-Gly) have been recorded and analyzed. The equilibrium geometry, bonding features and harmonic vibrational frequencies of L-Ala-Gly have been investigated with the help of B3LYP density functional theory (DFT) method. The calculated molecular geometry has been compared with the experimental data. The assignments of the vibrational spectra have been carried out with the help of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMFF). The optimized geometry shows the non-planarity of the peptide group of the molecule. Potential energy surface (PES) scan studies has also been carried out by ab initio calculations with B3LYP/6-311+G** basis set. The red shifting of NH3+ stretching wavenumber indicates the formation of N-H...O hydrogen bonding. The change in electron density (ED) in the sigma* antibonding orbitals and E2 energies have been calculated by natural bond orbital analysis (NBO) using DFT method. The NBO analysis confirms the occurrence of strong intermolecular hydrogen bonding in the molecule.     

B3LYP and MP2 calculations of the enthalpies of hydrogen-bonded complexes of methanol with neutral bases and anions: comparison with experimental data

To perfect a method for building a theoretical hydrogen-bond basicity scale, the enthalpy of hydrogen bonding between methanol and thirteen neutral and anionic bases (MeOH, MeNH2, Me2NH, Et2NH, Me3N, Et3N, Br-, CN-, SH-, Cl-, HCOO-, MeO-, F-) was calculated by DFT and ab initio methods. The theoretical results were compared to selected experimental ones. It appears that B3LYP/6-31+G(d,p) calculations are satisfactory for optimizing the geometry of complexes and giving a general order of basicity. However, they are deficient for reproducing the large effect of alkyl groups on the hydrogen-bond basicity of amines. This deficiency is explained by intermolecular perturbation theory calculations, which show that the alkylation of nitrogen dramatically increases the dispersion energy component not taken into account by the B3LYP functional. Of the methods considered, only MP2/aug-cc-pVTZ calculations are capable of reproducing the binding enthalpy within the experimental error for the first-row acceptor atoms N, O, and F, and of accounting for dispersion effects created by alkylation at the hydrogen-bond acceptor site.     

Temperature coefficient of NH chemical shifts of thioamides and amides in relation to structure

NH chemical shift temperature coefficients have been measured in a large series of N-substituted-3-piperidinethiopropionamides in which the NN distances are short but of varied length, as well as in a couple of the corresponding amides and in some simpler amides and thioamides. Geometries are calculated by means of ab initio DFT methods. The N-substituted-3-piperidinethiopropionamides show in most cases strong intramolecular N–HN hydrogen bonds according to IR spectra and ab initio calculations. For compounds with rather short NN distances the S=C–N–H moiety is non-planar. Dihedral angles as small as 160° are found. The NH chemical shift coefficients measured in non-polar solvents in all the N-substituted-3-piperidinethiopropionamides are more negative (−8 to −17 ppb/K) than in non-hydrogen bonded thioamides. For the latter in non-polar solvents like CDCl₃ and toluene the temperature coefficients are as small as −1 to −4 ppb/K. The large negative effects can be related not only to the non-planarity of the thioamide group in a way that the more pronounced the non-planarity the more negative the temperature coefficients, but also to strong hydrogen bonding and the fact that the acceptor is a nitrogen. For similar amides with non-planar amide groups and nitrogen acceptor large negative temperature coefficients are likewise seen. In polar solvents like DMF the effects in simple thioamides are uniform and close to −6 ppb/K, whereas in the more complex compound like 4p(t) the temperature coefficient is close to 0. An essential feature of measuring temperature coefficients of compounds without strong intramolecular hydrogen bonds in non-polar solvents and at low temperatures is to keep the concentration low enough to avoid dimerisation.     

Molecular structure, spectroscopic studies and first-order molecular hyperpolarizabilities of p-amino acetanilide

The infrared absorption, Raman spectra and SERS spectra of p-amino acetanilide have been analyzed with the aid of density functional theory calculations at B3LYP/6-311G(d,p) level. The electric dipole moment (mu) and the first hyperpolarizability (beta) values of the investigated molecule have been computed using ab initio quantum mechanical calculations. The calculation results also show that the synthesized molecule might have microscopic nonlinear optical (NLO) behavior with non-zero values. Computed geometries reveal that the PAA molecule is planar, while secondary amide group is twisted with respect to the phenyl ring is found, upon hydrogen bonding. The hyperconjugation of the C=O group with adjacent C-C bond and donor-acceptor interaction associated with the secondary amide have been investigated using computed geometry. The carbonyl stretching band position is found to be influenced by the tendency of phenyl ring to withdraw nitrogen lone pair, intermolecular hydrogen bonding, conjugation and hyperconjugation. The existence of intramolecular C=O...H hydrogen bonded have been investigated by means of the natural bonding orbital (NBO) analysis. The influence of the decrease of N-H and C=O bond orders and increase of C-N bond orders due to donor-acceptor interaction has been identified in the vibrational spectra. The SERS spectral analysis reveals that the large enhancement of in-plane bending, out of plane bending and ring breathing modes in the surface-enhanced Raman scattering spectrum indicates that the molecule is adsorbed on the silver surface in a 'atleast vertical' configuration, with the ring perpendicular to the silver surface.     

A bond-length-bond-order relationship for intermolecular interactions based on the topological properties of molecular charge distributions

Ab initio SCF MO calculations for the hydrogen-bonded complexes between nitriles and hydrogen fluoride suggest a strong linear relationship between the charge density at the hydrogen-bond critical point and the hydrogen-bond energy. Further investigation of the topological properties of the charge density indicates that the generalization of the bond-length-bond-order relationship of CC bonds due to Bader et al. may be extended to intermolecular hydrogen bonding. Calculations at the 6–31G^** level, including complete geometry optimization, are reported for the

complexes, where R  H, Li, F, Cl, HO, LiO, NC, HCC, CH₃ and CH₃O.     

Theoretical prediction of the hydrogen-bond basicity pK(HB)

Ab initio and DFT calculations on around 65 hydrogen bond or Lewis bases and their complexes with hydrogen fluoride have been performed, and a range of calculated properties from both free bases and complexes correlated with pK(HB), an experimental scale of hydrogen-bond basicity. For the entire range of bases, we found that the hydrogen-bond binding Gibbs free energy computed at the B3LYP/6-31+G(d,p) level of theory linearly correlated with pK(HB). Further improvements in the correlation and prediction of pK(HB) were possible with a non-linear fit by considering the hydrogen bonding Gibbs free energy of another possible stereoisomeric 1:1 complex and/or that of a linear 2:1 complex, which included a second hydrogen fluoride.     

Revealing the configuration and crystal packing of organic compounds by solid-state NMR spectroscopy: methoxycarbonylurea, a case study

The molecular configuration and intermolecular arrangement of polycrystalline methoxycarbonylurea (MCU) has been studied by a combination of chemical editing, rotational echo double resonance (REDOR) spectroscopy and ab initio calculations. From the multispin IS(n) REDOR experiments several dipolar couplings were determined and converted into distance constraints. Intra- and intermolecular dipolar couplings were distinguished by isotope dilution. The configuration of the MCU molecule can be determined from three torsion angles Psi1, Psi2, and Psi3. Ab initio calculations showed that these angles are either 0 degrees or 180 degrees (Z or E). From the REDOR experiments, the E configuration was found for Psi1 and Psi2 and the Z configuration for Psi3. Thus the configuration of MCU in the solid state was determined to be EEZ. Distance constraints for the intermolecular arrangement of MCU were obtained by performing REDOR experiments on 13C15N2 MCU with different degrees of isotope dilution and on a cocrystallized 1:1 mixture of 13C(urea) MCU and 15N(amide) MCU. By combining these distance constraints with molecular modeling, three different possible packing motifs for MCU molecules were found. The molecules in these motifs are arranged as linear chains with methoxy groups at the borders of the chains. All the intermolecular hydrogen bond donors and acceptors in the interior of the chain are saturated.     

Theoretical study of intermolecular spin alignments through hydrogen bonding of the carboxy group

Intermolecular magnetic interactions through hydrogen bonding of the carboxy group for dimers of allyl, benzyl, and chlorinated benzyl radicals have been investigated as model systems by the ab initio molecular orbital (MO) and density functional theory (DFT) calculations. It is found possible to propagate magnetic interaction through hydrogen bonding, although the effect is small. The spin densities of π- and σ-electrons have shown that antiferromagnetic coupling exists between the two intermolecular oxygen atoms in the ground state. This behavior is consistent with McConnell’s model, being applied to the planar configuration of the two hydrogen-bonded carboxy groups.     

Hydrogen bonding in high-resolution protein structures: a new method to assess NMR protein geometry

An analysis of backbone hydrogen bonds has been performed on nine high-resolution protein X-ray crystal structures. Backbone hydrogen-bond geometry is compared in the context of X-ray crystal structure resolution. A strong correlation between the hydrogen-bond distance, R(HO), and the hydrogen-bond angle, theta(NHO), is observed when the X-ray crystal structure resolution is <1.00 A. Ab initio calculations were performed to substantiate these results. The angle and distance limits found in our correlation for the backbone hydrogen-bond geometry can be used to evaluate the quality of protein structures and for further NMR structure refinement.     

Salicylaldehyde-indole-2-acylhydrazone: a simple,colorimetric and absorption ratiometric chemosensor for acetate ion

A simple anion receptor (i.e. salicylaldehyde-indole-2-acylhydrazone) was synthesised and its recognition properties were investigated by naked-eye observation, UV–vis titration spectra, ¹H NMR spectroscopy and DFT calculations. The obtained results indicated that this receptor could realise the selective colorimetric sensing and absorption ratiometric response towards AcO^?  in CH₃CN–DMSO medium, by virtue of threefold intermolecular hydrogen bonding interactions formed with phenolic OH, indole NH and amide NH.     

Modeling competitive interactions in proteins: vibrational spectroscopy of M+(n-methylacetamide)1(H2O)n=0-3, M=Na and K, in the 3 microm region

To properly understand the preferred structures and biological properties of proteins, it is important to understand how they are influenced by their immediate environment. Competitive intrapeptide, peptide...water, ion...water, and ion...peptide interactions, such as hydrogen bonding, play a key role in determining the structures, properties, and functionality of proteins. The primary types of hydrogen bonding involving proteins are intramolecular amide...amide (N-H...O=C) and intermolecular amide...water (O-H...O=C and H-O...H-N). n-Methylacetamide (NMA) is a convenient model for investigating these competitive interactions. An analysis of the IR photodissociation (IRPD) spectra of M+(n-methylacetamide)1(H2O)n=0-3 (M=Na and K) in the O-H and N-H spectral regions is presented. Ab initio calculations (MP2/cc-pVDZ) are used as a guide in identifying both the type and location of hydrogen bonds present. In larger clusters, where several structural isomers may be present in the molecular beam, ab initio calculations are also used to suggest assignments for the observed spectral features. The results presented offer insight to the nature of ion...NMA interactions in an aqueous environment and reveal how different ion...ligand pairwise interactions direct the extent of water...water and water...NMA hydrogen bonding observed.     

On the relative strengths of amide…amide and amide…water hydrogen bonds

We have performed Hayes—Stone intermolecular perturbation theory (IMPT) calculations on amide…water and amide…amide complexes in order to estimate the change ΔW in intermolecular interaction energy associated with the hydrogen bond exchange process amide(NH)…water+water…(OC)amideamide(NH)…(OC)amide+water…water. ΔW is found to be small and varies by almost 5 kJ/mol and in sign for the amides formamide, acetamide, N-methyl formamide and N-methyl acetamide. The main variations in the amide hydrogen bond energies occur in the electrostatic and exchange-repulsion contributions. This reflects the variation in the charge distributions of the hydrogen bonding groups between the different amides. Thus, we cannot quantify an isolated hydrogen bond strength with any great accuracy, and care must be used in extrapolating model potentials based on small model systems to peptides and proteins.     

A comparative ab initio study of methyl formate, methyl thiolformate and methyl thionoformate

Ab initio SCF-MO calculations have been carried out for HCOOCH₃, HC(=O)SCH₃ and HC(=S)OCH₃. Relative stabilities of s-trans/s-cis conformers are reported and discussed in terms of specific intramolecular interactions. The energy difference between the s-trans and the s-cis form increases in the order methyl thiolformate < methyl thionoformate < methyl formate. The major stabilizing factors of the s-cis forms are the bond dipolar interaction and the mesomeric delocalization through the five member ring involving both the X=C---Y---C (X, Y = O, S) skeleton and the out-of-plane hydrogen atoms. These effects are used to explain the trends mentioned. The non-planarity previously proposed for the thionoester is reinvestigated. Our calculations show that this molecule is planar. Molecular atomic charges, dipole moments and ionisation potentials are determined and compared with available experimental values.     

Molecular association in dimethyl sulfoxide-nitromethane mixtures: Raman spectroscopy and quantum-chemical calculations

Dimethyl sulfoxide-nitromethane (DMSO-NM) binary mixtures have been studied. Intermolecular associates are formed in these mixtures via the interaction between DMSO and NM molecular dipoles and hydrogen bonding. Ab initio calculations have been carried out at the MP2 perturbation theory level using the 6-31G(d, p) basis set to determine the optimal ground state geometry for DMSO complexes with NM and correctly assign new vibrational bands of molecules in various types of mixed intermolecular associates.     

Interaction between benzenedithiolate and gold: classical force field for chemical bonding

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as approximately 100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.     

Dependence of amide vibrations on hydrogen bonding

The effect of hydrogen bonding on the amide group vibrational spectra has traditionally been rationalized by invoking a resonance model where hydrogen bonding impacts the amide functional group by stabilizing its [(-)O-C=NH (+)] structure over the [O=C-NH] structure. However, Triggs and Valentini's UV-Raman study of solvation and hydrogen bonding effects on epsilon-caprolactum, N, N-dimethylacetamide (DMA), and N-methylacetamide (NMA) ( Triggs, N. E.; Valentini, J. J. J. Phys. Chem. 1992, 96, 6922-6931) casts doubt on the validity of this model by demonstrating that, contrary to the resonance model prediction, carbonyl hydrogen bonding does not impact the AmII' frequency of DMA. In this study, we utilize density functional theory (DFT) calculations to examine the impact of hydrogen bonding on the C=O and N-H functional groups of NMA, which is typically used as a simple model of the peptide bond. Our calculations indicate that, as expected, the hydrogen bonding frequency dependence of the AmI vibration predominantly derives from the C=O group, whereas the hydrogen bonding frequency dependence of the AmII vibration primarily derives from N-H hydrogen bonding. In contrast, the hydrogen bonding dependence of the conformation-sensitive AmIII band derives equally from both C=O and N-H groups and thus, is equally responsive to hydrogen bonding at the C=O or N-H site. Our work shows that a clear understanding of the normal mode composition of the amide vibrations is crucial for an accurate interpretation of the hydrogen bonding dependence of amide vibrational frequencies.     

Conformational stability of a model macrocycle tetraamide: an ab initio study

Ab initio calculations are carried out to investigate the conformational stability of a model macrocyle tetraamide. The four amide groups in the selected model are present in the sequence: -(O=CNH)-Ph-(NHC=O)-CH=CH-(O=CNH)-Ph-(NHC=O)-CH=CH-. In this sequence, two phenyl rings and two ethene groups act as bridges between the amide units. Each amide motif bonds to a phenyl ring through its amide nitrogen and to an ethene group through its amide carbon. Four clearly distinct minimum-energy conformations are found upon full geometry optimization using the B3LYP/6-31+G(d) method. Frequency calculations using the same method confirm that the four conformations are indeed minima in the macrocycle potential energy surface. Relative to the most stable conformer, the other conformations are higher in energy by 0.86, 2.09, and 9.17 kcal/mol, respectively, at the MP2/6-31+G(d,p) level. The stability of the macrocycle conformations is correlated primarily to the existence and strength of intramolecular N-H...O=C hydrogen bonds. Additional stability to the conformations is found to come from weak Ph-H...O=C hydrogen bonding between a carbonyl oxygen and a hydrogen atom of a phenyl group. Solvent effects play an important role in the relative energies of the various conformations, as indicated by the simple SCRF = dipole model calculations for the case of aqueous solution.     

A theoretical study of nonlinearity in heterocyclic hydrogen-bonded complexes

Ab initio calculations are performed at the MP2/6-311++G(d,p) and DFT/B3LYP/6-311++G(d,p) theoretical levels to obtain geometries, H-bond energies and harmonic infrared vibrational properties for the Cs symmetry structures of heterocyclic hydrogen-bonded complexes, CnHmY-HX. The H-bond lengths in DFT/B3LYP calculation level are in better agreement with the experimental values than the MP2 results. The geometry optimization are interpreted in terms of hydrogen bond nonlinearity represented by theta; and phi angles, once the hydrogen bond is formed among n-electrons pairs of the heteroatom in heterocyclic and the hydrogen atom in HX. The hydrogen bond energy after of the zero-point vibrational energy (ZPE) and basis set superposition error (BSSE) corrections are overestimated at DFT/B3LYP, whereas the MP2 BSSE corrections are very large than corresponding DFT/B3LYP. For example, the BSSE corrections for the C2H4S-HNC complex are 7.60 and 0.09 kJ mol(-1) in MP2 and DFT/B3LYP calculations levels, respectively. The new vibrational modes in infrared harmonic spectrum arising from complexation show several interesting features, especially the intermolecular stretching mode.     

The intramolecular hydrogen bond in 2-hydroxy-benzamides

The two crystal structures of 5-chloro-2-hydroxy-benzamide and 2-hydroxy-N,N-diethyl-benzamide were determined by X-ray diffraction at 100 K. The intramolecular and intermolecular hydrogen bonds were found in these structurally similar 2-hydroxy-benzamides. Analysis of the hydrogen bonding was carried out on the basis of X-ray data, infrared spectra, and DFT calculations. Disruption of the intramolecular hydrogen bonding in the solid state by a steric effect is shown. Conformational analysis and potential energy calculations as functions of the turning angle around the C_aryl–C_alkyl bond were conducted. The values obtained for the HOMA index indicate mutual compensation of the amide and hydroxyl groups (due to the high degree aromaticity of the phenyl ring).