Small interacting peptides. Part II: Interaction of cyclohexapeptides with immobilised model peptides. Comparison of infrared investigations, principal components analysis and force field calculations

The interaction of cyclic peptides with surface-bound model peptides was investigated by ATR-FTIR spectroscopy, principal components analysis and force field calculations. Information about the interacting functional COOH, COO-, and NH3+ groups and the peptide backbone was gained through a set of cyclohexapeptides (seven of the type c(X1KX2KX3K) (K = L-lysine) and one of the type c(X1KX2KX3k) (k = D-lysine), which are interacting with L-arginine- or tripeptide-coated Si-ATR crystals. All measurements were performed in aqueous solutions. Spectra evaluation in the range 1800-1500 cm(-1) was done by band and principal components analysis (PCA). Only adsorbed molecules were present in these spectra. The coatings were investigated by ATR-FTIR spectroscopy too in order to characterise their functional groups. Based on this knowledge, the spectra of the interacting partners could be evaluated in relation to cyclohexapeptides and coatings. As a result, it was possible to identify the distinct differences in the bonding behaviour of the various peptides.     

Interaction of an infrared surface plasmon with an excited molecular vibration

The interaction of an infrared surface plasmon and an excited molecular vibration was investigated by using a square array of subwavelength holes in a Ni film which supports propagating, surface-plasmon-mediated, transmission resonances. The largest transmission resonance [the (1,0)(-)] was tuned through the rocking vibration of the hexadecane molecule (at 721 cm(-1)) in a hexadecane film on the mesh by varying the thickness of the film. The interaction of the rocking vibration and surface plasmon is characterized spectroscopically by an increase in the intensity of the vibrational band by more than a factor of 2, variation of the vibrational line shape relative to the spectrum on a nonmetallic surface, and shifts in vibrational peak position by as much as 3.0 cm(-1). Relationships are developed between the transmission resonance position and the thickness and dielectric properties of the coating.     

Interactions of phosphorylated cyclohexapeptides with uranyl: insights from experiments and theoretical calculations

Two phosphorylated cyclohexapeptides (CPs) bearing one (CP1) or two phosphates (CP2) were synthesized to explore the interactions between uranyl ions and very small cyclic peptides. According to the results of the ESI–MS and fluorescence titrations, the 1:1 uranyl-CPs complexes are the main products with the affinity constants of 7.3?×?10⁴ and 2.0?×?10⁵ for CP1 and CP2, respectively. Density functional theory calculations indicate phosphoryl and carboxyl groups coordinate uranyl in mono-dentate and bi-dentate fashions due to steric effects, which is consistent with the results of extended X-ray absorption fine structure spectroscopy.

     

Self-consistent optimization of molecular geometries by semi-empirical force field method : Part I. Computational scheme

A force field method based on the semi-empirical force approach is used to predict the completely optimized geometries of both the stationary and the saddle points on the molecular energy hyper-surface. The computational aspects are discussed and the organization of computer programs is briefly described. The convergence properties are examined based on the results obtained from MINDO theory.     

Interaction of organic molecules with the TiO2 (110) surface: ab inito calculations and classical force fields

We have studied the adsorption of a number of organic molecules consisting of methyl, benzyl, and carboxylic groups on the rutile TiO2 (110) surface using both ab initio and atomistic simulation techniques. We have tested the applicability of a simple embedded cluster model to studying the adsorption of small organic molecules on the perfect rutile TiO2 (110) surface, and used this model to develop a classical force field for the interactions of a wide class of organic molecules consisting of these groups with the rutile TiO2 (110) surface. The force field accounts for physisorption and ionic bonding of organic molecules at the surface. It allows the reproduction of adsorption energies and of geometries of organic molecules on the rutile surface. It should be useful for studying diffusion of these molecules and their manipulation with use of AFM and STM tips.     

Ab initio calculations of carbon‐containing species and comparison with group additivity results: Part I. C5 species

Twenty‐six C₅ compounds and radicals related to combustion processes have been calculated using the ab initio G3//B3LYP method using the atomization enthalpy analysis. The results have been compared to group additivity estimates and literature values where available. Three different group additivity programs were used, and results concerning the comparison are given. The NIST 94 program is more reliable than the other two. © 2007 Wiley Periodicals, Inc. Int J Chem Kinet 39: 620–628, 2007     

Interaction of water molecules with the electric field of an ionic-crystal surface

A theoretical investigation of the coulombic interaction of water molecules with an ideal surface of an ionic crystal is conducted. The calculation is based on the Fourier transform of the long-range part of an coulombic potential with subsequent summation of its Fourier images and tabulation of the results. The method is numerically tested when solving the problem concerning the interaction with the surface of a silver iodide crystal. A comparison of the electric field near an ideal crystalline surface and its finite fragment is performed. The data obtained point to a strong dependence of electrochemical properties of the surface on the presence of crystalline defects on it.     

Polarizable Simulations with Second order Interaction Model (POSSIM) force field: Developing parameters for alanine peptides and protein backbone

A previously introduced POSSIM (POlarizable Simulations with Second order Interaction Model) force field has been extended to include parameters for alanine peptides and protein backbones. New features were introduced into the fitting protocol, as compared to the previous generation of the polarizable force field for proteins. A reduced amount of quantum mechanical data was employed in fitting the electrostatic parameters. Transferability of the electrostatics between our recently developed NMA model and the protein backbone was confirmed. Binding energy and geometry for complexes of alanine dipeptide with a water molecule were estimated and found in a good agreement with high-level quantum mechanical results (for example, the intermolecular distances agreeing within ca. 0.06?). Following the previously devised procedure, we calculated average errors in alanine di- and tetra-peptide conformational energies and backbone angles and found the agreement to be adequate (for example, the alanine tetrapeptide extended-globular conformational energy gap was calculated to be 3.09 kcal/mol quantim mechanically and 3.14 kcal/mol with the POSSIM force field). However, we have now also included simulation of a simple alpha-helix in both gas-phase and water as the ultimate test of the backbone conformational behavior. The resulting alanine and protein backbone force field is currently being employed in further development of the POSSIM fast polarizable force field for proteins.     

Potential energy surface exploration with equilibrial paths. Part I: Theory

The equilibrial path concept is further developed. Special attention is spent the symmetry conservation along equilibrial paths and symmetry-breaking. Symmetry-breaking can occur only at singular points. The simple singular points of an equilibrial path are valley–ridge inflection points. In contrast to the intrinsic reaction paths and the gradient extremal paths, the equilibrial paths enable to describe the branching of reaction channels.     

Derivation of class II force fields: V. Quantum force field for amides,peptides, and related compounds

As the field of biomolecular structure advances, there is an ever-growing need for accurate modeling of molecular energy surfaces to simulate and predict the properties of these important systems. To address this need, a second generation amide force field for use in simulations of small organics as well as proteins and peptides has been derived. The critical question of what accuracy can be expected from calculations in general, and with this class II force field in particular, is addressed for structural, dynamic, and energetic properties. The force field is derived from a recent methodology we have developed that involves the systematic use of quantum mechanical observables. Systematic ab initio calculations were carried out for numerous configurations of 17 amide and related compounds. Relative energies and first and second derivatives of the energy of 638 structures of these compounds resulted in 140,970 ab initio quantum mechanical observables. The class II peptide quantum mechanical force field (QMFF), containing 732 force constants and reference values, was parameterized against these observables. A major objective of this work is to help establish the role of anharmonicity and coupling in improving the accuracy of molecular force fields, as these terms have not yet become an agreed upon standard in the ever more extensive simulations being used to probe biomolecular properties. This has been addressed by deriving a class I harmonic diagonal force field (HDFF), which was fit to the same energy surface as the QMFF, thus providing an opportunity to quantify the effects of these coupling and anharmonic contributions. Both force field representations are assessed in terms of their ability to fit the observables. They have also been tested by calculating the properties of 11 stationary states of these amide molecules. Optimized structures, vibrational frequencies, and conformational energies obtained from the quantum calculations and from both the QMFF and the HDFF are compared. Several strained and derivatized compounds including urea, formylformamide, and butyrolactam are included in these tests to assess the range of applicability (transferability) of the force fields. It was found that the class II coupled anharmonic force field reproduced the structures, energies, and vibrational frequencies significantly more faithfully than the class I harmonic diagonal force field. An important measure, rms energy deviation, was found to be 1.06 kcal/mol with the class II force field, and 2.30 kcal/mol with the harmonic diagonal force field. These deviations represent the error in relative configurational energy differences for strained and distorted structures calculated with the force fields compared with quantum mechanics. This provides a measure of the accuracy that might be expected in applications where strain may be important such as calculating the energy of a system as it approaches a (rotational) barrier, in ligand binding to a protein, or effects of introducing substituents into a molecule that may induce strain. Similar results were found for structural properties. Protein dynamics is becoming of ever-increasing interest, and, to simulate dynamic properties accurately, the dynamic behavior of model compounds needs to be well accounted for. To this end, the ability of the class I and class II force fields to reproduce the vibrational frequencies obtained from the quantum energy surface was assessed. An rms deviation of 43 cm⁻¹ was achieved with the coupled anharmonic force field, as compared to 105 cm⁻¹ with the harmonic diagonal force field. Thus, the analysis presented here of the class II force field for the amide functional group demonstrates that the incorporation of anharmonicity and coupling terms in the force field significantly improves the accuracy and transferability with regard to the simulation of structural, energetic, and dynamic properties of amides. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 430–458, 1998     

Benchmark database on isolated small peptides containing an aromatic side chain: comparison between wave function and density functional theory methods and empirical force field

A detailed quantum chemical study on five peptides (WG, WGG, FGG, GGF and GFA) containing the residues phenylalanyl (F), glycyl (G), tryptophyl (W) and alanyl (A) -- where F and W are of aromatic character -- is presented. When investigating isolated small peptides, the dispersion interaction is the dominant attractive force in the peptide backbone-aromatic side chain intramolecular interaction. Consequently, an accurate theoretical study of these systems requires the use of a methodology covering properly the London dispersion forces. For this reason we have assessed the performance of the MP2, SCS-MP2, MP3, TPSS-D, PBE-D, M06-2X, BH&H, TPSS, B3LYP, tight-binding DFT-D methods and ff99 empirical force field compared to CCSD(T)/complete basis set (CBS) limit benchmark data. All the DFT techniques with a '-D' symbol have been augmented by empirical dispersion energy while the M06-2X functional was parameterized to cover the London dispersion energy. For the systems here studied we have concluded that the use of the ff99 force field is not recommended mainly due to problems concerning the assignment of reliable atomic charges. Tight-binding DFT-D is efficient as a screening tool providing reliable geometries. Among the DFT functionals, the M06-2X and TPSS-D show the best performance what is explained by the fact that both procedures cover the dispersion energy. The B3LYP and TPSS functionals-not covering this energy-fail systematically. Both, electronic energies and geometries obtained by means of the wave-function theory methods compare satisfactorily with the CCSD(T)/CBS benchmark data.     

Theoretical investigations of structure and enzymatic mechanisms of aspartyl proteinases : Part I. Ab-initio calculations on an active site model: hydrogen diformiate with H2O and H3O

The active site of aspartyl proteinases (Asp) was modelled as two formiates connected with a proton and set in geometry corresponding to Asp 32 and Asp 215 side chain carboxylate groups of endothiapepsin. The shared solvent molecule was alternatively H₂O and H₃O⁺. Their positions and those of hydrogen-bonded protons were optimized using the STO-3G basis set. Full geometry optimizations were made of the hydrogen diformiate complexes with H₂O and H₃O⁺. Asymmetric hydrogen-bonded structures resulted from these calculations, except for the fully optimized complex with H₂O. In the complexes with H₃O⁺, one proton moved consistently to the proximate carboxylic oxygen yielding a neutral, hydrated formic acid dimer. Interaction energies and proton potential energy curves were calculated using the 4-31G basis set. The interaction energy with H₂O was found to be 20.49 kcal mol⁻¹ and 202.75 kcal mol⁻¹ with H₃O⁺.     

High-resolution infrared measurements of v1 and force field calculations for thioborine (HBS)

The gas-phase high-resolution spectrum is reported for v₁ of the linear molecule thioborine (HBS) from 2775 cm^?1 to 2720 cm^?1. Band centers and rotational constants are given for the 10⁰0-00⁰0 transitions of H¹¹B³²S, H¹⁰B³²S, H¹¹B³⁴S and H¹⁰B³⁴S and for the 11¹0-01¹0 transitions of H¹¹B³²S and H¹⁰B³²S. A valence force field is determined from measured values of v₁, D_o (the centrifugal distortion) and q (the l-doubling constant). The remaining unobserved vibrational fundamentals are calculated from the force constants.     

Vibrational spectra and force field of azacyclic compounds. I. Pyrrole

For the molecules of pyrrole and its symmetric deuterated derivatives, vibrational spectra have been analyzed, and the force field has been defined in natural coordinates.Translated from Khimiya Geterotsiklicheskikh Soedinenii, Vol. 29, No. 5, pp. 651–655, May, 1993.     

Application of force field calculations—III: Conformational isomerism and dynamic gearing in ethanes with many alkyl substituents. EFF calculations and dynamic NMR measurements

Force-field calculations and dynamic NMR measurements of symmetrical 1,2-dialkyl-1,1,2,2-tetramethylethanes where the alkyl group is methyl, ethyl, isobutyl, neopentyl, isopropyl, cyclohexyl, or t-butyl are reported. There is usually slightly less than one third of the population in the anti-conformation, slightly more than two thirds in gauche conformations but the t-butyl compound adopts only the anti-conformation. Barriers to rotation vary markedly between 8.1 and 13.8kcal/mol, being lower for secondary alkyl groups than for primary alkyl groups. Calculations suggest that rotation about the central bond and rotation of the secondary alkyl group, by taking place in a concerted fashion, produce several rotational itineraries of similar energies. The low barrier is thus due to a favourable entropy effect.     

Electrochemical investigations in non-aqueous media : Part I. Investigation of the dissociation of dibasic acids

The stoichiometric dissociation constants of seven dibasic acids were determined in four alcohols by potentiometric titration; it was assumed that the acidic and neutral salts dissociate completely. A linear relationship was found between the pK_1.2 values of dibasic acids in water and those in alcohols.     

Compact basis sets for LCAO-LSD calculations. Part I: Method and bases for Sc to Zn

A method for preparing compact orbital and auxiliary basis sets for LCAO-LSD calculations has been developed. The method has been applied to construct basis sets for first row transition metal atoms from Sc to Zn for the 3d^n?14s¹ and 3d^n?24s² configurations. The properties of different expansion patterns have been tested in atomic calculations for the chromium atom.     

Early evolution of gas adsorption chromatography. Part I: Displacement development and the beginnings of elution-type investigations

Summary This two-part article reviews the early evolution of gas-adsorption chromatography, before the advent of partition chromatography. After reporting on the early tests to determine the light hydrocarbon content of natural gas and the methodology described by P.Schuftan, the research activities of S. Claesson and C.S.G. Phillips on displacement-type gas-adsorption chromatography and early work on elution-type analysis by G. Damk?hler, E. Wicke, E. Glueckauf and G. Hesse are discussed. Part II of this review article will be published in the forthcoming issue ofChromatographia.     

The molecular structure of S-triazine in the gas phase determined from electron diffraction, infrared/raman data and ab initio force field calculations

The gas phase molecular structure of s-triazine has been determined from electron diffraction data. Experimental vibrational parameters proved consistent with those from the 4-21G force field after scaling onto infrared/Raman frequencies, as well as after direct scaling on electron diffraction data. The analysis resulted in the following r_g/r^°-parameters CN = 1.338(1) Å, CH = 1.106(8) Å, CNC = 113.9(1), NCN = 126.1, HCN = 116.9. The (new) r_g – r_e (4-21G) correction for aromatic CN is 0.006(1) Å.