Vibrational molecular force field of model compounds with biologic interest. II. Harmonic dynamics of both anomers of glucose in the crystalline state

Combining the modified Urey–Bradley–Shimanouchi intramolecular potential energy function with an appropriate intermolecular energy function, normal coordinate calculations have been performed for both α and β anomers of glucose and for some deuterated analogs in the crystalline state. The overall agreement between the observed and calculated frequencies leads to an average error on the order of 3 and 5 cm^?1 for α and β glucose, respectively. In both cases, it is shown that the intermolecular potential energy terms are essential to reproduce perfectly the whole spectra, in particular for the hydroxyl stretching region, the anomeric and crystalline spectral regions, and the low-frequency range. Moreover, the intermolecular interactions have a nonnegligible influence on the value of the intramolecular force constants. But, the potential energy distribution of vibrational modes are in accord with previous works performed for an isolated molecule. It is also important to point out that approximately the same set of force constants has been used for both molecules, differences existing only for the atoms involved in the anomeric configuration. Likewise, different charge distributions have been calculated and tested with different value of the dielectric constant. Charges determined by the AM₁ quantum mechanical procedure with a value of 3 for the dielectric constant have the merit to reproduce quite well the whole spectra and in particular the frequency range below 200 cm^?1. © 1993 John Wiley & Sons, Inc.     

Force field and vibrational spectra of oligosaccharides with different glycosidic linkages—Part II. Maltose monohydrate,cellobiose and gentiobiose

Complete Raman and IR spectra of maltose monohydrate, cellobiose and gentiobiose have been recorded in the crystalline state. These three disaccharides present the same monosaccharide composition of the glucose molecule and the remaining studied position (1–4 and 1–6) of the glycosidic linkage. Moreover, maltose and cellobiose present the different configurations of the glycosidic linkage α, 1–4 and β, 1–4, respectively. These data will constitute the support for theoretical calculations of normal modes of vibration. The assignments of the calculated bands of vibration will be made on the basis of the potential energy distributions using a modified Urey—Bradley—Shimanouchi intramolecular potential energy combined with a specific intermolecular potential energy function. The calculations show that using a correct initial force field, it is possible to reproduce correctly the density of observed vibrational states for large molecules such as disaccharides. The standard deviation between calculated and observed frequencies, below 1500 cm⁻¹, leads to values of 4.7, 4.2 and 4.6 cm⁻ for maltose monohydrate, cellobiose and gentiobiose, respectively. Our previous investigations on trehalose dihydrate, sophorose monohydrate and laminaribiose are confirmed in this study and complete the previous assignments for the whole set of disaccharides.     

A potential function for computer simulation studies of proton transfer in acetylacetone

A potential energy model is developed to study the intramolecular proton transfer in the enol form of acetylacetone. It makes use of the empirical valence bond approach developed by Warshel to combine standard molecular mechanics potentials for the reactant and product states to reproduce the interconversion between these two states. Most parameters have been fitted to reproduce the key features of an ab initio potential surface obtained from 4-31G^* Hartree-Fock calculations. The partial charges have been fitted to reproduce the electrostatic potential surface of 6-31G^* Hartree-Fock wave functions, subject to total charge and symmetry constraints, using a fitting procedure based on generalized inverses. The resulting potential energy function reproduces the features most important for proton transfer simulations, while being several orders of magnitude faster in evaluation time than ab initio energy calculations. © 1997 by John Wiley & Sons, Inc.     

Potential energy functions for an intramolecular proton transfer reaction in the ground and excited state

We describe the development of empirical potential functions for the study of the excited state intramolecular proton transfer reaction in 1-(trifuloroacetylamino)-naphtaquinone (TFNQ). The potential is a combination of the standard CHARMM27 force field for the backbone structure of TFNQ and an empirical valence bond formalism for the proton transfer reaction. The latter is parameterized to reproduce the potential energies both in the ground and the excited state, determined at the CASPT2 level of theory. Parameters describing intermolecular interactions are fitted to reproduce molecular dipole moments computed at the CASSCF level of theory and to reproduce ab initio hydrogen bonding energies and geometries for TFNQ-water bimolecular complexes. The utility of this potential energy function was examined by computing the potentials of mean force for the proton transfer reactions in the gas phase and in water, in both electronic states. The ground state PMF exhibits little solvent effects, whereas computed potential of mean force shows a solvent stabilization of 2.5 kcal mol⁻¹ in the product state region, suggesting proton transfer is more pronounced in polar solvents, consistent with experimental findings. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Contribution to the Fernando Bernardi Memorial Issue.     

Normal coordinates analyses of beta-D-allose and alpha-D-talose in the crystalline state

IR and Raman spectra of beta-d-allose, alpha-d-talose and beta-d-allose O-D(5) have been recorded in the 4000-400 cm(-1) and in the 4000-20 cm(-1) regions. These spectra constitute the experimental support that allows to reproduce theoretically the vibrational frequencies and to establish a force field for these saccharides through a normal coordinate analysis. For this purpose, a modified UBSFF has been combined with an intermolecular potential energy function that includes the Van der Walls interactions, the electrostatic terms, and an explicit hydrogen bond function. The initial force field parameters are derived either from those of D-glucose or D-galactose and are fitted so as to obtain a good agreement between the calculated and the observed frequencies. The obtained results reproduce the experimental frequencies and in order to test the validity of the obtained force field, it has been applied to beta-D-allose O-D(5).     

Low-temperature electron transfer in bacterial photosynthesis

The role of a continuous medium frequency distribution of the Debye form in low-temperature thermal electron transfer processes is investigated. When the electrons are strongly coupled to the medium (the medium reorganization energy is 0.2–0.4 eV) a temperature-independent rate constant is predicted from zero temperature up to over 100 K and with far-infrared Debye frequencies. This is compatible with the experimentally observed low-temperature branch in the Arrhenius relationship of the electron transfer from cytochrome c to excited bacteriochlorophyll, Bch⁺, in bacterial photosynthesis. However, in order to reproduce the high-temperature branch, of finite activation energy, additional activation of intramolecular modes of higher frequencies must be assumed. An intramolecular mode of a coupling constant of 8–9 and a frequency of about 400 cm^?1 can account for this branch. Finally, the estimated electron exchange integral is about 10^?4 eV, indicating that the process is strongly a none diabetic.     

Interaction of Lysine-Alanine-Alanine tripeptide with a fragment of DNA: An empirical potential study

Interaction of a rigid fragment of B-DNA (polyanionic as well as screened by Na⁺ cations) with the flexible tripeptide Lys-Ala-Ala (in both L and D configurations) were investigated with the aid of an empirical potential. The potential consists of intramolecular (MM2 potential) and intermolecular (pair potential described in reference 1) parts; hence total energy is formed by intra- and intermolecular components. The results demonstrate that intramolecular relaxation of the peptide results in a considerable decrease in total energy. While energies of DNA complexes with L-Lys-L-Ala-L-Ala were comparable to those with D-Lys-D-Ala-D-Ala the respective geometries exhibit considerable differences.     

Vibrational spectra,normal modes,force field and barrier to inversion of phosphiran,phosphiran-1-d1 and phosphiran-2,3-d4

The infrared spectra over the range of intramolecular fundamentals of polycrystalline phosphiran and phosphiran-1-d₁ at 77 °K have been obtained and the observed frequencies assigned. Correlation field effects have been observed and analyzed in terms of the intermolecular forces operative in the unit cell. The intramolecular vibrations of phosphiran, phosphiran- 1-d₁, and phosphiran-2,3-d₄ have been subjected to simultaneous analysis in the approximation of harmonic forces and the resulting eigenvectors and potential energy distributions are presented. An estimate from the force field of the periodic barrier with inversion at phosphorus of 33 kcal mole^?1 has been obtained and compared to results for similar molecules. Thermodynamic functions for phosphiran have been calculated in the rigid rotor harmonic oscillator approximation.     

Quantum-Chemical and semiclassical calculations of intermolecular interactions of phospholipids

By use of empirical 0–1–6–12 atom–atom potential functions and the PCILOCC method intra- and intermolecular interactions of glycero–phosphoryl–ethanolamine model head groups in a planar layer crystal were calculated. Starting from investigations of the two-dimensional energy-contour diagrams the minima of energy as a function of all head group torsion angles were calculated using a gradient procedure. Within an interval of 15 kcal/mol above the energy of the global minimum we obtained about 30 local minima. These results demonstrate a high flexibility of the investigated phosphorylethanolamine head group in agreement with experiment. The ethanolamine moiety exists in enantiomeric conformations. With the torsion angles of the 0–1–6–12 energy minimization procedure PCILOCC calculations were carried out. These calculations yield the x-ray conformation as the most stable one (unit-cell stabilization energy = ?36.3 kcal/mol). The PCILOCC as well as the potential function calculations show that the conformation of phospholipid head groups in layer crystals is determined by intramolecular as well as by intermolecular interactions with neighboring phospholipid molecules.     

Spectroscopy of H 3 + with energies above the barrier to linearity: rovibrational transitions in the range of 10,000–14,000 cm−1

Based on a recently extended potential energy surface for H ₃ ⁺ with a highly reliable form of the topology of the surface far beyond the barrier to linearity, rovibrational frequencies in the range of 10,000–14,000 cm^?1 have been derived and are compared with new experiments. The computed transition frequencies reproduce experimental transitions mostly within a few tenths of a wavenumber, if non-adiabatic effects are crudely simulated using different reduced masses for vibrational and rotational motions. Deviations can only be compensated if non-adiabatic effects are treated more rigorously.     

Hormone-receptor-relationships: synthesis and characteristics of N-epsilon-dansyllysine 21-adrenocorticotropin-(1-24)-tetrakosipeptide

We are investigating interactions between hormones and their potential receptor molecules by means of biologically active, synthetic hormone derivatives. The substituents are so chosen that they can supply quantitative information about specific contacts or convert the hormone to an ‘affinity marker’. We describe the synthesis of N^ε-dansyllysine²¹-adrenocorticotropin-(1–24)-tetrakosipeptide. In fat cells and in adrenal cells of the rat the dansyl substituent does not seem to impair the interaction between the peptide moiety and its biological receptors. It allows for affinity studies by fluorescence depolarisation and for measurement of intramolecular and intermolecular distances by means of energy transfer (fluorescence sensibilisation).     

Electrochemical Synthesis of Heterocyclic Compounds II. Synthesis of Some N-Heterocycles by Intramolecular Oxidative Cyclisation

Electrochemical intramolecular and intermolecular cyclisations as well as reactions occurring with expansion or contraction of rings have been reviewed^2–5. Sometimes, electrochemical oxidative or reductive cyclisations have considerable advantages when compared with other chemical methods^6-8     

Prototropic behavior of cyclohexane substituted urethane and urea compounds. Observation of H-bond mediated 4HJH1H3 coupling constants across urea fragments

Two 1-aryl-3-cyclohexylurea and two 1-aryl-3-cyclohexylurethane with and without alkyl tail in aryl fragments were synthesized and their variable-temperature ¹H NMR spectra in chloroform, DMSO and DMF were recorded. The temperature dependences of chemical shift of NH protons for all compounds have been observed. The type of dependence has been explained by the aggregation of molecules and formation of ionic structures. The formation of intermolecular complexes leads to possible formation of symmetrical N1 ^{… …} H ^……N3 intramolecular hydrogen bond in urea fragment. As a result,^4hJ_H1H3 trans-hydrogen bond scalar coupling constants have been observed for the first time in low molecular weight compounds using a simple one-dimensional ¹H NMR experiment. The formation of strong intramolecular H-bond leads to π-conjugation not only with spacer but with phenyl ring too. It support the Gilli conception that RAHB formation is a result of π-electron delocalization. The presence in urea fragment of such kind interaction leads to formation of ionic structure, which has been detected by NMR and UV spectroscopies. The formation of ionic structure can explain the catalytic activity of such compounds and the mechanism of transformation in organic and bioorganic reactions in which involved the urea compounds.     

A heuristic potential function for intramolecular and intrasupermolecular chemical reactions

A heuristic fitting procedure to obtain an analytical potential function for describing a reactive potential energy surface in the neighborhood of the intrinsic reaction coordinate (IRC ) has been developed. For discussion, the pairwise potential function form, ∑a_nr^?n, is assumed in order to fit ab initio quantum mechanical calculations of intramolecular (or intrasupermolecular) interaction energies and its use is found advantageous because all the calculation can be carried out by the linear least squares method. Normal modes perpendicular to IRC are utilized to prepare an initial data base for the potential fitting in the neighborhood of IRC . Some trial molecular dynamics (MD ) simulations are performed in order to check the fitted potential function and, unless they lead to reasonable energies within the tolerance assumed, their results are utilized to construct an improved data base (the dynamic sampling). The present systematic optimization procedure has been applied to the proton transfer reaction of the formamidine–water (FW ) system. The normal mode analysis in both the transition state (TS ) and the stable state (SS ) regions suggests that the present fitted potential function can reproduce satisfactorily the Born–Oppenheimer (BO ) adiabatic surface obtained by ab initio molecular orbital (MO ) calculations. We conclude that our procedure works well for the chemical reaction molecular dynamics (CRMD ) simulation.     

Description of the influence of intermolecular interaction on IR spectra's frequencies of simple dense fluids by Monte-Carlo simulation

The solvent-induced shift in IR spectrum of liquid CO is investigated by Monte-Carlo computer simulation. The intramolecular potential is Morse function, pair intermolecular potential includes short-range and dispertion parts. The calculated shift is 5 cm^?1 while the experimental value is 4 cm^?1.     

Probing intermolecular couplings in liquid water with two-dimensional infrared photon echo spectroscopy

Two-dimensional infrared photon echo and pump probe studies of the OH stretch vibration provide a sensitive probe of the correlations and couplings in the hydrogen bond network of liquid water. The nonlinear response is simulated using numerical integration of the Schrodinger equation with a Hamiltonian constructed to explicitly treat intermolecular coupling and nonadiabatic effects in the highly disordered singly and doubly excited vibrational exciton manifolds. The simulated two-dimensional spectra are in close agreement with our recent experimental results. The high sensitivity of the OH stretch vibration to the bath dynamics is found to arise from intramolecular mixing between states in the two-dimensional anharmonic OH stretch potential. Surprisingly small intermolecular couplings reproduce the experimentally observed intermolecular energy transfer times.     

A spectroscopically effective molecular mechanics model for the intermolecular interactions of the hydrogen-bonded N-methylacetamide dimer

An MP2/6-31+G¹ calculation of the N-methylacetamide dimer shows that it has two minimum energy structures, both hydrogen bonded with peptide planes roughly perpendicular to each other. A complete molecular mechanics optimization of the dimer has been done, using a model for the intermolecular interactions consisting of charges, atomic dipoles, and van der Waals interactions and the methodology of our spectroscopically determined force field for the intramolecular interactions. The two structures are satisfactorily reproduced, as are their interaction energies, their dipole moments, and, from the point of view of our goal of a spectroscopically accurate force field, their six intermolecular normal mode frequencies.     

Quantification of Noncovalent Interactions in Azide–Pnictogen, –Chalcogen,and –Halogen Contacts

The noncovalent interactions between azides and oxygen-containing moieties are investigated through a computational study based on experimental findings. The targeted synthesis of organic compounds with close intramolecular azide–oxygen contacts yielded six new representatives, for which X-ray structures were determined. Two of those compounds were investigated with respect to their potential conformations in the gas phase and a possible significantly shorter azide–oxygen contact. Furthermore, a set of 44 high-quality, gas-phase computational model systems with intermolecular azide–pnictogen (N, P, As, Sb), –chalcogen (O, S, Se, Te), and –halogen (F, Cl, Br, I) contacts are compiled and investigated through semiempirical quantum mechanical methods, density functional approximations, and wave function theory. A local energy decomposition (LED) analysis is applied to study the nature of the noncovalent interaction. The special role of electrostatic and London dispersion interactions is discussed in detail. London dispersion is identified as a dominant factor of the azide–donor interaction with mean London dispersion energy-interaction energy ratios of 1.3. Electrostatic contributions enhance the azide–donor coordination motif. The association energies range from −1.00 to −5.5 kcal mol⁻¹.