Ab initio calculations on Pro-Ala and Pro-Gly dipeptides

The geometries of the dipeptides -Pro- -Ala, -Pro- -Ala and -Pro-Gly were investigated by a grid scan ab initio calculation. The 6-31G basis set was used to estimate the effect of the alanyl side-chain on the conformation of the peptide backbone and to provide a computational basis for the interpretation of known physical-chemical properties of larger peptides that contain these dipeptides. These calculations furnish a direct quantum mechanical assessment of the energetic consequences of a methyl side-chain in the i + 2 position of a turn. The results of the calculation support the current view that the presence of a -Ala residue in the i + 2 position favors a type II β-turn over a type I β-turn conformation, while -Ala has the opposite effect. Total and relative energies for all the optimized conformations identified by the grid search are given and geometric parameters (bond lengths, bond angles and dihedral angles) and net atomic charges have been calculated.     

A molecular dynamics study of the pentacyclo-undecane cage amino acid tripeptide

In this paper, we report on the conformational profile of the pentacyclo-undecane (PCU) cage tripeptide carried out by molecular dynamics (MD) simulation using water as an explicit solvent. The MD solution phase studies carried on the model peptide analogues (A)=Ac–Ala–Ala–Ala–NHMe; (B)=Ac–Cage–Cage–Cage–NHMe; (C)=Ac–Ala–Cage–Ala–NHMe and (D)=Ac–Ala–Pro–Ala–NHMe, are used as a complimentary technique to the corresponding gas phase simulated annealing (SA) study previously carried out in our laboratory. No significant structural changes were observed over the MD trajectories. However, the results reported here provide further evidence that the (PCU) cage amino acid exhibits C_7eq, C_7aq, _R and _L conformations, and the theoretical results suggest that the PCU cage amino acid is a strong β-turn inducer. These results support the prediction that when the PCU cage residues are in the (i) and (i+2) positions, the β-turn can be extended in either direction to form anti-parallel β-pleated sheets, thereby forming the basis of the mechanism for the folding back of the chain in a cross-β-turn structure.     

Quantum theory of the structure and bonding in proteins : Part 14. The serine dipeptide

The energies of the conformations of the serine dipeptide are computed by ab initio molecular orbital theory in order to demonstrate the existence of the hydrogen bonds, torsion barriers and non-bonded repulsions which govern the relative energies of these conformations. The Ramachandran map of the dipeptide is computed and found to resemble closely those of alanine and ethyl glycine. The side-chain maps are them computed and analysed to show the above physical effects in terms of the torsion barrier-free maps.

There is generally good agreement between the experimental and theoretical results in the sense that all three side-chain conformations which are staggered about CC^β (₁ = + 60, 180 and −60°) are computed to be close in energy and all three values of ₁ occur with similar frequencies in the proteins examined. The fact that serine, unlike all other comparable residues except threonine, tends to favour a ₁ value of + 60° in the bridge region is reproduced clearly by the computations and analysis of the physical factors involved shows that this conformation is stabilised by side chain to backbone hydrogen bonding.     

QTAIM study of the closed-shell interactions in peptide secondary structures: A cluster treatment of oligo- and polyalanines

The closed-shell interactions in oligo- and polyalanines are studied by the quantum theory of atoms in molecules (QTAIM) using electron densities derived from the B3LYP/6-31+G^** ground-state electronic wave-functions. The QTAIM enabled us to identify a large number of the intraturn closed-shell stabilizing interactions in the β-turns, which were presented by several conformers of the tetrapeptide model compound. We found that only β-turn type IVa exhibits a 10-member pseudocycle. The intrachain H-bonds between the adjacent N–H and CO groups in the antiparallel β-sheet conformation of polyalanine have not been found. At the same time, these interactions do exist in the parallel conformation and are even stronger than the interchain N–H…O bonds. A weak interaction between the CO group at the position i and the side-chain C–H group at the position i + 3 was detected in the -helical conformation of polyalanine.     

Electronic structure and conformational properties of the amide linkage Part 5. Internal rotation and inversion in 1-formylaziridine

Internal rotation and nitrogen inversion in 1-formylaziridine (1) have been investigated by quantum mechanical (ab initio and MNDO) calculations, especially with respect to the variation of the geometry of the aziridine ring. While conformational stability is mainly determined by the n(N)/π(CO) interaction, the bond lengths within the ring are affected by the amount of interaction between the π(CO) orbital and the Walsh orbital ω_A. To separate the two types of interaction, calculations were also performed on formylcyclopropane (9). The torsional potential of 1 has a minimum close to the perpendicular conformation 1b. The two bisected conformations, 1a and 1c, are transition states for internal rotation. For nitrogen inversion, a barrier of 1.44 kcal mol⁻¹ (ab initio) was calculated. Calculations on 1-cyanoaziridine (7) gave inversion barriers of 5.81 (ab initio) and 12.31 kcal mol⁻¹ (MNDO). Probably due to methodical reasons the ab initio values seem to be too low, as calculations with different basis sets for aziridine indicate.     

Vibrational spectroscopic detection of H-bonded β- and γ-turns in cyclic peptides and glycopeptides

The conformation of N-glycoproteins and N-glycopeptides has been the subject of many spectroscopic studies over the past decades. However, except for some preliminary data, no detailed study on the vibrational spectroscopy of glycosylated peptides has been published until recently.

This paper reports FTIR spectroscopic properties in DMSO and TFE of the N-glycosylated cyclic peptides cyclo[Gly-Pro-Xxx(GlcNAc)-Gly-δ-Ava] 3a and 3b in comparison with data on the non-glycosylated parent peptides cyclo(Gly-Pro-Xxx-Gly-δ-Ava) 2a and 2b [a, Xxx = Asn; b, Xxx = Gln; δ-Ava = NH-(CH₂)₄-CO] and N-acetyl 2-acetamido-2-deoxy-β- -gluco pyranosylamine (GlcNAc-NHAc, 4). The assignment of amide I band frequencies to conformation is based on ROESY experiments and determination of the temperature coefficients in DMSO-d₆ solution. (For the synthesis and NMR characterization of 2a and 3a see Ref. [19].)

Cyclic peptides are expected to adopt folded (β- and/or γ-turn) conformations which may be fixed by intramolecular H-bonding(s). A comparison of the temperature coefficients of the NH protons and amide I band frequencies and intensities suggests that in DMSO there is no significant difference in the backbone conformation and H-bond system of the N-glycosylated models and their parent cyclic peptides. The common feature of the backbone conformation of models 2 and 3 is the predominance of a 1 ← 4 (C₁₀) H-bonded type II β-turn encompassing Pro-Xxx or Pro-Xxx(GlcNAc), respectively. The ROESY connectivities in the Asn(GlcNAc) model (3a) have not been found to reflect intramolecular H-bondings between the peptide and the sugar.

The unique feature of the FTIR spectra in DMSO of the cyclic models is the lack or weakness of low-frequency (< 1640 cm⁻¹) amide I component bands. In TFE the amide I region of the FTIR spectra shows an increased number of components below 1650 cm⁻¹ reflecting a mixture of open and H-bonded β- and γ-turn conformers.

Because of its destabilizing effect upon γ-turns and other weakly H-bonded structures, DMSO decreases the number of backbone conformers. DMSO also destroys side-chain-backbone H-bondings of type C₇, C₆ or C₈. Possible ‘glyco’ C₇ H-bondings in GlcNAc-NHAc (4) or in glycopeptides 3a and 3b cannot resist the effect of DMSO either.

The FTIR data in TFE of models 2–4 suggest that the acceptor amide group of strong C₇ H-bondings in peptides and glycopeptides absorbs at 1630 ± 5 cm⁻¹ and that of bifurcated H-bondings between 1600–1620 cm⁻¹.     

Quantum theory of the structure and bonding in proteins : Part 15. The threonine dipeptide

The energies of the conformations of the threonine dipeptide are determined by adding the energetic effects of the methyl group to the results for the serine dipeptide. The results are then checked by explicit ab initio molecular orbital computations on the important low-energy conformations. Analysis of these results yields the non-bonded repulsions, the torsion barriers and the hydrogen bonds.

There are many similarities between the serine results and those for threonine. In particular, the computations show that the +60° value of χ ₁ is again important in the helix bridge region of the Ramachandran map. On the other hand, there is a pronounced difference between serine and threonine in that the methyl group of the latter causes the form with χ₁ = 180° to be a high-energy conformation over all areas of the Ramachandran map except the left sheet region. These and other points are in accord with the experimental data for five proteins.     

Fourfold clusters of rovibrational energies in H2Te studied with an ab initio potential energy function

We report here an ab initio investigation of the cluster effect (i.e., the formation of four-member groups of nearly degenerate rotation-vibration energy levels at higher J and K_a values) in the H₂Te molecule. The potential energy function has been calculated ab initio at a total of 334 molecular geometries by means of the CCSD (T) method where the (1s-4f) core electrons of the Te atom were described by an effective core potential. The values of the potential energy function obtained cover the region up to around 10 000 cm⁻¹ above the equilibrium energy. On the basis of the ab initio potential, the rotation-vibration energy spectra of H₂ ¹³⁰Te and its deuterated isotopomers have been calculated with the MORBID (Morse oscillator rigid bender internal dynamics) Hamiltonian and computer program. In particular, we have calculated the rotational energy manifolds for J40 in the vibrational ground state, the ν₂ state, the “first triad” (the ν₁/ν₃/2 ν₂ interacting vibrational states), and the “second triad” (the (ν₁ + ν₂)/(ν₂ + ν₃)/3 ν₂ states) of H₂¹³⁰Te. We have also investigated the cluster formation in the vibrational ground state of H₂ ¹³⁰Te by first fitting the rotational data available from experiment with a modified Watson-type effective Hamiltonian and then using the optimized ground state constants to extrapolate the rotational structure to higher J values. Both the ab initio calculation and the prediction with the effective Hamiltonian show that the cluster formation in H₂Te is very similar to that in H₂Se and H₂S, which we have studied previously. However, contrary to semiclassical predictions, we do not determine any significant displacement of the clusters towards lower J values relative to H₂Se. Hence the experimental observation of the cluster states in H₂Te will be at least as difficult as in H₂Se.     

Ab initio analysis of the conformational changes of the prolyl-proline model peptide

For- -Pro- -Pro-NH₂ is an ab initio model of the prolyl-proline sequence unit present in numerous peptides and proteins. Cis–trans isomerization of the peptide linkage is a crucial step in accessing the active conformation of several proline containing macromolecules.

The present study focuses on the flexibility of the five-membered pyrrolidine ring, which is considered to help other conformational changes as well as cis–trans isomerization. Ring flexibility is characterized by the pseudorotational amplitude, A, and the phase angle, P. Calculations are carried out at the RHF/6-31+G(d) level of theory. The choice of method and level of theory is further supported by single point DFT calculations.

In the course of NMR structure determination of peptides or proteins, proline residues present in the sequences need special attention. Because of the lack of an amide hydrogen, sequential assignment of proline is rather complicated. Furthermore, in solution state, peptide cis–trans isomers are almost always present. Ab initio study on the For- -Pro- -Pro-NH₂ model is a useful tool to discover the structural characteristics of the prolyl-proline sequence unit.     

CSSP2: an improved method for predicting contact-dependent secondary structure propensity

The calculation of contact-dependent secondary structure propensity (CSSP) has been reported to sensitively detect non-native β-strand propensities in the core sequences of amyloidogenic proteins. Here we describe a noble energy-based CSSP method implemented on dual artificial neural networks that rapidly and accurately estimate the potential for the non-native secondary structure formation in local regions of protein sequences. In this method, we attempted to quantify long-range interaction patterns in diverse secondary structures by potential energy calculations and decomposition on a pairwise per-residue basis. The calculated energy parameters and seven-residue sequence information were used as inputs for artificial neural networks (ANNs) to predict sequence potential for secondary structure conversion. The trained single ANN using the >(i, i ± 4) interaction energy parameter exhibited 74% accuracy in predicting the secondary structure of test sequences in their native energy state, while the dual ANN-based predictor using (i, i ± 4) and >(i, i ± 4) interaction energies showed 83% prediction accuracy. The present method provides a simple and accurate tool for predicting sequence potential for secondary structure conversions without using 3D structural information.     

Conformational properties of azapeptides

The conformation of several model compounds for azapeptides was systematically examined on the basis of ab initio MO theory at various approximation levels. The calculations show the azapeptide conformation essentially determined by the hydrazine and urea constituents along the sequence. This leads to a characteristic conformer pattern which excludes the possibility of β sheet conformations, but indicates a high potency for the formation of helix and β turn structures. The N atom may change between planar and pyramid structures. The peculiar conformation properties make azaamino acids an attractive tool for secondary structure design in peptides and proteins.     

Rhenium(I) methoxo carbonyl complexes containing tetraphosphine or triphosphine ligands; facile separation and X-ray crystallographic studies of d/l- and meso-[{Re2(μ-OMe)2(CO)6}2(μ,μ′-1,1,4,7,10,10-hexaphenyl-1,4,7,10-tetra-phosphadecane)]

Reaction of the activated mixture of Re₂(CO)_10, Me₃NO and MeOH with a 1:1 mixture of rac (d/l)- and meso-1,1,4,7,10,10-hexaphenyl-1,4,7,10-tetraphosphadecane (hptpd) yields a mixture of (d/l)- and meso-[{Re₂(μ-OMe)₂(CO)₆}₂(μ,μ′-hptpd)] 1. The diastereomers can be easily separated by selective dissolution of d/l-1 in benzene, and give clearly distinguishable ¹H- and ³¹P-NMR spectra. The fluxional behavior of d/l-1 in solution has been studied by variable-temperature ¹H- and ³¹P-{¹H}-NMR spectroscopy. The crystal structures of both d/l- and meso-1 have been determined. Both molecules consist of two {Re₂(μ-OMe)₂(CO)₆} moieties which are bridged by the two P---CH₂---CH₂---P moieties of the hptpd ligand. Whilst the molecules of meso-1 possess crystallographic i-symmetry, those of d/l-1 do not have any crystallographic symmetry. These diastereomers therefore give clearly distinguishable Raman spectra in the solid state. Reaction of tris[2-(diphenylphosphino)ethyl]phosphine (tdppep) with the activated mixture affords the complex [{Re₂(μ-OMe)₂(CO)₆}(μ,η²-tdppep)] 2, and the analogous reaction involving bis[2-diphenylphospinoethyl)phenylphosphine (triphos) gives [{Re₂(μ-OMe)₂(CO)₆}(μ,μ′,η³-triphos){Re₂(CO)₉}] 3 and [{Re₂(μ-OMe)₂(CO)₆}(μ,η²-triphos)] 4.     

Binding of acrylic and sulphonic polyanions by open-chain polyammonium cations

The interactions between some acrylic and sulphonic polyanions and some protonated amines (diamines NH₂-(CH₂)_x-NH₂, x=2,…,10; linear tri-, tetra-, penta- and hexa-amines) were studied potentiometrically in aqueous solution, at 25°C. For both types of polyanions AL₂H_i (L⁻, monomer of polyanion, A, amine) species are formed, with i=1,…,n (n=number of amino groups in the amine). The stability of these species is strictly dependent on the polyammonium cation charge, and fairly independent of the type of amine (in diamine species maximum stability is observed for x=4, 5). Acrylic and sulphonic polyanion complexes are considerably stronger than analogous species formed by low molecular weight anions. Mean stability can be expressed as log K=2.87ζ^2/3, for polyacrylic anions and log K=2.42ζ^2/3 for polysulphonic anions (ζ=absolute value for charge product of reactants).     

Oxidative addition of organic halides to zerovalent palladium complexes containing rigid bidentate nitrogen ligands

Zerovalent complexes of the type Pd(Ar-BIAN)(alkene), i.e. complexes containing the rigid bidentate nitrogen ligands bis(arylimino) acenaphthene (Ar = p-Tol, p-MeOC₆H₄, o-Tol,o,o′-Me₂C₆H₃, o,o′-ⁱPr₂C₆H₃) and an electron-poor alkene have been shown to react with a variety of (organic) halides RX, including methyl, benzyl, aryl, acyl and allylic halides, to give the corresponding square planar divalent Pd(R)X(Ar-BIAN) or [Pd(η³-allyl)(Ar-BIAN)]X complexes. The new complexes obtained have been fully characterized and their fluxional behaviour in solution studied by ¹H NMR spectroscopy. The rate of oxidative addition of iodomethane to Pd(p-Tol-BIAN)(alkene) complexes was found to decrease with increasing Pd-alkene bond strength, i.e. dimethyl fumarate fumaronitrile, but oxidative addition to the fumaronitrile complex was accelerated by irradiation with a mercury lamp. Oxidative addition of allylic ha     

Cis- and trans-3-hexene: infrared spectrum in liquid argon solution, ab initio calculations of equilibrium geometry, normal coordinate analysis, and vibrational assignments

The infrared spectra of cis-3-hexene and trans-3-hexene dissolved in liquid argon have been obtained at temperatures from 93 to 120 K. The absorptions were observed with a low-temperature cell and a Fourier transform infrared spectrophotometer. Ab initio molecular orbital calculations were performed to obtain the equilibrium geometry, vibrational frequencies, force fields, and infrared intensities. The calculations were done at the Hartree-Fock level using 6-31G basis set. The Cartesian force fields from ab initio calculations have been converted to the force field in symmetry coordinates. The scale factors of ab initio calculated force fields were determined. Normal coordinate calculations were performed using a scaled quantum mechanical (SQM) force field. Vibrational normal modes calculated for the lowest energy rotamers of cis- and trans-3-hexene have been assigned to infrared absorption bands observed in liquid argon solution. The assignments were based on calculated frequencies and potential energy distributions. The equilibrium geometries of the two lowest energy rotamers (symmetry C₂ and C_s) of cis-3-hexene and of the three lowest energy rotamers (symmetry C_i, C₂, and C₁) of trans-3-hexene were calculated. Variable temperature studies of the infrared spectrum of cis- and trans-3-hexenes dissolved in liquid argon were done to obtain the ΔH of conversion between the rotamers C₂ and C_s of cis-3-hexene and between the rotamers C_i, C₂, and C₁ of trans-3-hexene.     

On the vibrational spectra and conformational stability of 1,1-dimethylhydrazine from temperature dependent FT-IR spectra of krypton solutions and ab initio calculations

Variable temperature (−105 to −150 °C) studies of the infrared spectra (3500–400 cm⁻¹) of 1,1-dimethylhydrazine, (CH₃)₂NNH₂, in liquid krypton have been carried out. No convincing spectral evidence could be found for the trans conformer which is expected to be at least 600 cm⁻¹ less stable than the gauche form. The structural parameters, dipole moments, conformational stability, vibrational frequencies, and infrared and Raman intensities have been predicted from MP2/6-31G(d) ab initio calculations. The predicted infrared and Raman spectra are compared to the experimental ones. The adjusted r₀ parameters from MP2/6-311+G(d,p) calculations are compared to those reported from an electron diffraction study. The energy differences between the gauche and trans conformers have been obtained from MP2 ab initio calculations as well as from density functional theory by the B3LYP method calculations from a variety of basis sets. All of these calculations indicate an energy difference of 650–900 cm⁻¹ with the B3LYP calculations predicted the larger values. The potential function governing the conformational interchange has been predicting from both types of calculations and comparisons have been made. The barrier to internal rotation by the independent rotor model of the inner methyl group is predicted to have a value of 1812 cm⁻¹ and that of the outer one of 1662 cm⁻¹ from ab initio MP2/6-31G(d) calculations. These values agree well with the experimentally determined values of 1852±16 and 1558±12 cm⁻¹, respectively, from a fit of the torsional transitions with the coupled rotor model. For the coupled rotor model the predicted V′₃₃ (sin 3τ₀ sin 3τ₁ term) value which ranged from 190 to 232 cm⁻¹ is in reasonable agreement with the experimental value of 268±3 cm⁻¹ but the predicted V₃₃ (cos 3τ₀ cos 3τ₁ term) value of −73 to −139 cm⁻¹ is 25% smaller and of the opposite sign of the experimental value of 333±22 cm⁻¹. These theoretical and spectroscopy results are compared to similar quantities of some corresponding molecules.     

Beryllocene, (C5H5)2Be. The He(I) photoelectron spectrum and ab initio molecular orbital calculations

Ab initio molecular orbital calculations with a double-ζ basis have been carrried out on five models of beryllocene, Cp₂Be, with fixed geometries. The lowest energies are obtained for the π-Cp, σ-Cp and D_5d models.

The He(I) photoelectron spectrum of Cp₂Be was recorded and the ionization potentials of the first bands were compared with the orbital energies obtained from the molecular orbital calculations. A satisfactory fit between experiment and calculations was obtained for a slip sandwich model of C_s symmetry. A model of C_5v symmetry is only compatible with the PE spectrum if the Jahn—Teller splitting of the lowest ²E₁ state of the molecular ion is exceptionally large, 1.0 eV.     

Exchange interaction energy between two one-active electron atoms at large distances

Developed formulas for the exchange interaction energy between two neutral one-active electron atoms interacting at large distances R are presented in terms of known basic integrals obtained from an asymptotic method for the alkali dimers M₂ dissociating to M(ns) + M(ns), M(n′l) + M(n′l), l = 0, …, 3 and M (np) + M(np). Detailed illustrative numerical results are displayed for the molecular states of Na₂ dissociating to the limit Na(3s) + Na(3p). Comparisons with very accurate ab initio results as well as with some available experimental data show that accurate potential energy curves for these excited states may be obtained in a very large range of internuclear distances by connecting ab initio curves for small and intermediate values of R with long-range curves obtained as the sum of usual multipolar Coulombic energy and asymptotic exchange energy.     

Zn NMR investigation of zinc halides

⁶⁷Zn NMR has been used as a probe to measure the electric field gradients at the metal site in the zinc halides ZnF₂, γ-ZnCl₂, ZnBr₂ and ZnI₂ and Rb₂ZnCl₄ at room temperature. In addition two hydration states have been detected for ZnSO₄. For ZnF₂ and γ-ZnCl₂ an ab initio calculation of the electric field gradient at the Zn site using the W 97 code agrees well with the experimentally observed values.     

Adsorption of polyacrylic acid on aluminium oxide: DRIFT spectroscopy and ab initio calculations

Diffuse reflectance Fourier transform infrared (DRIFT) spectroscopy was used to study the adsorption process of the water-soluble polyacrylic acid (PAA) polymer on hydrous δ-Al₂O₃. Vibrational assignment of PAA, sodium polyacrylate, (Na–PA) and the PA-oxide surface complex was achieved by comparison of observed band position and intensity in the DRIFT spectra with wavenumbers and intensities from ab initio quantum mechanical calculations. The presented data of polyacrylic acid suggest that IR data calculated ab initio on relatively short oligomers (quantum-mechanical oligomer approach) may provide valuable information regarding the interpretation of polyelectrolyte infrared spectra. Batch adsorption experiments were performed to sorb PAA onto the δ-Al₂O₃ surface. The results obtained from DRIFT studies were compared with adsorption isotherm experiments in order to relate the level of PAA coverage to the nature of the surface complex. Ab initio molecular orbital calculations on PAA/Al₂O₃ clusters were used to model possible surface complexes. Strong correlation were found between theoretical and observed DRIFT frequencies of the antisymmetric R-COO⁻ vibration. A number of possible configurations of the polyacrylic acid/aluminate surface complex were tested via ab initio calculations. These possible configurations included different di-aluminium octahedral Al³⁺ surface models. Results obtained from adsorption isotherm experiments, DRIFT spectra and ab initio calculations indicate that the carboxylate oxygens bridge an Al³⁺-octahedral dimer [Al₂(OH)₂4(H₂O)2(OH)] in a ligand-exchange inner sphere complex.