Extended electron distributions applied to the molecular mechanics of some intermolecular interactions

Summary Extended electron distributions (XEDs) have been added to the molecular mechanics Coulombic term and applied to a selection of intermolecular interactions. The results from this approach have been compared with the commonly used atom-centred charges and more rigorous AM1-derived natural atom orbital point densities. The use of XEDs generally improves the simulation of experimental and ab initio results over the other two charge allocations and corrects geometries in those cases for which the others yield wrong results.     

A computational study of the Diels-Alder reaction of ethyl-S-lactyl acrylate and cyclopentadiene. Origins of stereoselectivity

The eight diastereoisomeric transition structures of the Diels-Alder addition of ethyl-S-lactyl acrylate and cyclopentadiene have been investigated in the gas phase and in solution by HF, MP2, and density functional theory (B3LYP and B3PW91) methods with the 6-31G(d,p) basis set. At all levels of theory used, the s-cis transition structures are more stable than the s-trans ones. The contribution of the s-trans transition structures increases in solution and, although still small, has to be taken in consideration for correct prediction of stereoselectivity. Diastereofacial selectivity is interpreted in terms of electrostatic (weak hydrogen bonding) C=O...H(C) interactions between the carbonyl group(s) of the dienophile and cyclopentadiene in the energetically favored transition structures. Endo/exo reaction selectivity is attributed to positive orbital interactions between the diene and the acrylate carbonyl oxygen in the endo s-cis transition structures. Ab initio methods reproduce well the experimentally observed trends in both endo/exo and diastereofacial selectivity. Density functional calculations in the gas phase correctly reproduce the observed trends in diastereofacial selectivity but single-point MP2 calculations are necessary to reproduce the experimental trend in endo/exo selectivity.     

Combining a polarizable force-field and a coarse-grained polarizable solvent model. II. Accounting for hydrophobic effects

A revised and improved version of our efficient polarizable force-field/coarse grained solvent combined approach (Masella, Borgis, and Cuniasse, J. Comput. Chem. 2008, 29, 1707) is described. The polarizable pseudo-particle solvent model represents the macroscopic solvent polarization by induced dipoles placed on mobile pseudo-particles. In this study, we propose a new formulation of the energy term handling the nonelectrostatic interactions among the pseudo-particles. This term is now able to reproduce the energetic and structural response of liquid water due to the presence of a hydrophobic spherical cavity. Accordingly, the parameters of the energy term handling the nonpolar solute/solvent interactions have been refined to reproduce the free-solvation energy of small solutes, based on a standard thermodynamic integration scheme. The reliability of this new approach has been checked for the properties of solvated methane and of the solvated methane dimer, as well as by performing 10 × 20 ns molecular dynamics (MD) trajectories for three solvated proteins. A long-time stability of the protein structures along the trajectories is observed. Moreover, our method still provides a measure of the protein solvation thermodynamic at the same accuracy as standard Poisson-Boltzman continuum methods. These results show the relevance of our approach and its applicability to massively coupled MD schemes to accurately and intensively explore solvated macromolecule potential energy surfaces.     

A vibrational molecular force field of model compounds with biological interest. I. Harmonic dynamics of crystalline urea at 123 K

Normal coordinate calculations have been performed for urea and deuterated urea in the crystalline state. We have used the modified Urey–Bradley–Shimanouchi intramolecular potential energy function and a rather sophisticated intermolecular energy function to reproduce I.R. and Raman frequencies with an average error of 2 cm^–1. The general agreement between the calculation and experiment suggests that intermolecular interactions must be taken into account to determine reliable intramolecular parameters of the potential energy function, mainly the barrier to internal rotation around the C? N bond. The intermolecular energy function, which consists of the Buckingham function and an explicit harmonic function for hydrogen-bonding, then has the merit to reproduce quite well the observed frequencies of lattice vibrations.     

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).     

Methodology for the calculation of the potential of mean force for a cation-pi complex in water.

We report potential of mean force (PMF) calculations on the interaction between the p-sulfonatocalix[4]arene and a monovalent cation (Cs(+)). It has been recently shown from microcalorimetry and (133)Cs NMR experiments that the association with Cs(+) is governed by favourable cation-pi interactions and is characterized by the insertion of the cation into the cavity of the macrocycle. We show that the PMF calculation based upon a classical model is not able to reproduce both the thermodynamic properties of association and the insertion of the cation. In order to take into account the different contributions of the cation-pi interactions, we develop a new methodology consisting of changing the standard PMF by an additional contribution resulting from quantum calculations. The calculated thermodynamic properties of association are thus in line with the microcalorimetry and (133)Cs NMR experiments and the structure of the complex at the Gibbs free-energy minimum shows the insertion of the cation into the cavity of the calixarene.     

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.     

Multiple peptide conformations give rise to similar binding affinities: molecular simulations of p53-MDM2

Molecular dynamics simulations, guided by experimental information (Zondlo et al. Biochemistry 2006, 45, 11945-11957) have been used successfully to reproduce experimental trends in binding affinities of variant p53 peptides with MDM2. Simulations reveal how the conformations of the peptides and the receptor modulate each other to optimize interactions. The conformations of the uncomplexed peptides are governed by a combination of helix and intrinsic disorder (in agreement with experiments), while in the complexed state two very different conformations can coexist. This yields very similar binding affinities, driven by either enthalpy or entropy.     

Vibrational spectra and gas phase structure of N-cyanoimidosulfurous difluoride, NCN=SF2

The vibrational spectra, IR (gas) and Raman (liquid) of N-cyanoimidosulfurous difluoride, NCN=SF2, were recorded, and the molecular structure was determined by gas electron diffraction. The spectra were assigned by comparing the vibrational frequencies with those in related molecules and with calculated (HF, MP2, B3LYP with 6-31G(d) basis sets) values, and a normal coordinate analysis was performed. The molecule possesses a syn conformation (Ctriple bondN syn with respect to the bisector of the SF2 angle). This has been rationalized by orbital interactions of the electron lone pairs of sulfur and nitrogen with the N-C and S-F bonds, respectively, which are antiperiplanar or anticlinal to these lone pairs (anomeric effects). Quantum chemical calculations with the B3LYP and MP2 methods reproduce the experimental structure reasonably well if large basis sets (6-311G(2d,f)) are used.     

Specific interactions in complexes formed by DNA and conducting polymer building blocks: guanine and 3,4-(ethylenedioxy)thiophene

In the present paper we report direct experimental evidence of the existence of hydrogen bonds between poly(3,4-(ethylenedioxy)thiophene) (PEDOT) and DNA complexes and bring deeper knowledge about how such interactions can take place in such species. To this end, we used both experimental and theoretical methodologies to examine the interactions between the building blocks composing these two macromolecules. The specific interaction natures between 3,4-(ethylenedioxy)thiophene (EDOT, E) and doubly protonated guanine (GH(2)(2+)) monomers have been investigated using UV-vis spectroscopy. Quantum mechanical calculations in the density functional theory (DFT) and time-dependent density functional theory (TDDFT) frameworks have been used to identify the structures of the possible complexes. These differ in the interaction pattern, and it was possible to interpret the absorption spectra in terms of intermolecular interactions. Our results allow verification of the previous hypothesis about the formation of specific N-H···O interactions between G-containing nucleotide sequences and PEDOT. Clearly, DFT calculations indicate that E:GH(2)(2+) complexes are stabilized by N-H···O interactions, which involve an E oxygen and the -NH and -NH(2) moieties of GH(2)(2+). Furthermore, TDDFT calculations are able to reproduce the absorption spectra (both energy gaps and relative oscillator strength magnitudes) of E and GH(2)(2+), as well as the complex.     

Theoretical calculation of structures and proton transfer in hydrated ammonia-hydrogen chloride clusters

Ab initio molecular orbital calculations have been performed to investigate the structures and quantum effects of the proton motion in NH(3):HCl:(H(2)O)(n) (n = 0-3) clusters using a MP2/aug-cc-pVDZ level of theory. Three new stable structures and one transition-state structure are investigated for these clusters. The detailed analyses of the intermolecular interactions suggest that three-body interactions play an important role to determine the relative stability in each size of cluster. The quantum effects of the proton motion result in frequency shifts for proton-stretching modes. Our one-dimensional and two-dimensional models fairly closely reproduce the experimental proton-stretching vibrational frequency of the NH(3):HCl cluster. The most stable isomer for n = 1 has a proton-transfer structure, which is weakened by the quantum effects of the proton motion.     

Frenkel‐exciton decomposition analysis of circular dichroism and circularly polarized luminescence for multichromophoric systems

Recently, a method to calculate the absorption and circular dichroism (CD) spectra based on the exciton coupling has been developed. In this work, the method was utilized for the decomposition of the CD and circularly polarized luminescence (CPL) spectra of a multichromophoric system into chromophore contributions for recently developed through‐space conjugated oligomers. The method which has been implemented using rotatory strength in the velocity form and therefore it is gauge‐invariant, enables us to evaluate the contribution from each chromophoric unit and locally excited state to the CD and CPL spectra of the total system. The excitonic calculations suitably reproduce the full calculations of the system, as well as the experimental results. We demonstrate that the interactions between electric transition dipole moments of adjacent chromophoric units are crucial in the CD and CPL spectra of the multichromophoric systems, while the interactions between electric and magnetic transition dipole moments are not negligible. © 2018 Wiley Periodicals, Inc.     

A new force field for atomistic simulations of aqueous tertiary butanol solutions

We present a new tert-butanol force field parametrized to reproduce the mixture thermodynamics of tert-butanol/water over a wide range of solution compositions at room temperature and atmospheric pressure. The experimental Kirkwood-Buff integrals, which quantify preferential solvation of solution components by the same species or by the other components, were used as target values to be reproduced. Water was modeled using the simple point charge model. In the range of alcohol mole fractions between 0.02 and 0.98, our optimized model satisfactorily reproduces alcohol-alcohol, water-water, and alcohol-water aggregation behavior. As a consequence, the solution activity derivatives are reproduced as well. A comparison has been made with solution activities obtained by free energy calculations (i.e., thermodynamic integration). It clearly shows that the Kirkwood-Buff based approach performs superior in predicting solution activities of liquid mixtures. The new tert-butanol model has been used to examine the solution structure and hydrophobic interactions in aqueous tert-butanol at the various mixture compositions. A comparison is made with structural data obtained by neutron diffraction.     

On the use of common effective core potentials in density functional calculations. I. Test calculations on transition-metal carbonyls

The performance of effective core potentials adjusted at the Hartree-Fock level but applied in density functional calculations has been tested in a set of calculations using various basis sets and/or core potentials. Test molecules have been the first-row transition-metal carbonyls Cr(CO)₆, Fe(CO)₅, and Ni(CO)₄ and the second-row carbonyls Mo(CO)₆, Ru(CO)₅, and Pd(CO)₄. Only “small-core” potentials have been used, and these are able to reproduce molecular structures and bond energies from all-electron calculations. Relativistic effects have been estimated for the second-row carbonyls by using quasi-relativistic core potentials. © 1996 John Wiley & Sons, Inc.     

Adenine versus guanine quartets in aqueous solution: dispersion-corrected DFT study on the differences in π-stacking and hydrogen-bonding behavior

We have investigated the performance of the dispersion-corrected density functionals (BLYP-D, BP86-D and PBE-D) and the widely used B3LYP functional for describing the hydrogen bonds and the stacking interactions in DNA base dimers. For the gas-phase situation, the bonding energies have been compared to the best ab initio results available in the literature. All dispersion-corrected functionals reproduce well the ab initio results, whereas B3LYP fails completely for the stacked systems. The use of the proper functional leads us to find minima for the adenine quartets, which are energetically and structurally very different from the C_4h structures, and might explain why adenine has to be sandwiched between guanine quartets to form planar adenine quartets.     

Chromatographic models for the sorption of neutral organic compounds by soil from water and air.

The solvation parameter model is used to construct models for the estimation of the soil-water and soil-air distribution constants and to characterize the contribution of fundamental intermolecular interactions to the underlying sorption processes. Wet soil is shown to be quite cohesive and polar but relatively non-selective for dipole-type, lone-pair electron and hydrogen-bond interactions. Using a comparison of system constant ratios chromatographic systems employing reversed-phase liquid chromatography on polar bonded phases are shown to provide suitable models for estimating soil-water distribution constants. No suitable gas chromatographic models were found for the soil-air distribution constant but the requirements for such a system are indicated. Models are also provided for adsorption at the air-water interface. Estimation methods based on either the solvation parameter model or chromatographic model reproduce experimental distribution constants for a wide variety of compounds with a similar error (0.2-0.3 log units) to that expected in the experimental data.     

Derivation of force field parameters for SnO2-H2O surface systems from plane-wave density functional theory calculations

Plane-wave density functional theory (DFT-PW) calculations were performed on bulk SnO2 (cassiterite) and the (100), (110), (001), and (101) surfaces with and without H2O present. A classical interatomic force field has been developed to describe bulk SnO2 and SnO2-H2O surface interactions. Periodic density functional theory calculations using the program VASP (Kresse et al., 1996) and molecular cluster calculations using Gaussian 03 (Frisch et al., 2003) were used to derive the parametrization of the force field. The program GULP (Gale, 1997) was used to optimize parameters to reproduce experimental and ab initio results. The experimental crystal structure and elastic constants of SnO2 are reproduced reasonably well with the force field. Furthermore, surface atom relaxations and structures of adsorbed H2O molecules agree well between the ab initio and force field predictions. H2O addition above that required to form a monolayer results in consistent structures between the DFT-PW and classical force field results as well.     

Synthesis and preferred all-syn conformation of C3-symmetrical N-(hetero)arylmethyl triindoles

A new series of C(3)-symmetrical N-(hetero)arylmethyl triindoles has been synthesized in a straightforward procedure. The structure and conformation in the solid state have been determined for three derivatives (3, 4, and 6) by X-ray crystallographic analysis. In all three cases, the molecules adopt a tripodal conformation with all of the flexible arms directed towards the same side, thereby delimiting an inner cavity. Compound 6 crystallizes and forms C(3)-symmetric dimeric cagelike complexes. Guest molecules of chloroform and water are confined within the resulting cavities with stabilization by different intermolecular interactions; this highlights the potential of these compounds in the construction of supramolecular systems. A computational analysis has been performed to predict the most stable conformers. As a general trend, a preference for a conformation with all branches directed to the same side has been predicted. Comparison between theoretical and experimental results indicates that the computational level selected for the present study, B3LYP/6-31G*, is able to reproduce both the minimum energy conformations and the rotation barriers about the N--CH(2) bond.     

Group electronegativity and Fukui function studies of the substituent effects in aromatic and inorganic systems

The group electronegativities (GE ) of molecular fragments, including the environmental contributions due to both the electrostatic interactions and electron distribution relaxation, and the Fukui function (FF ) indices of the charge sensitivity analysis (CSA ) are correlated with the known substituent effects in molecular systems. The semiempirical CSA in the atoms-in-molecules (AIM ) resolution has been applied to substituted benzenes and square platinum complexes treated as illustrative examples. The calculated FF indices and GE are both shown to constitute adequate reactivity criteria that qualitatively reproduce the known substituent effects. The FF index (second-order property) is found to be a more sensitive detector of the substituent influence than is the corresponding GE parameter (first-order property). © 1992 John Wiley & Sons, Inc.