CONFORMATIONAL CHARACTERISTICS OF POLY(ACRYLIC ACID) AND POLY(METHACRYLIC ACID)

A full-relaxation optimization of molecule and the Dreiding force field are employed toobtain the geometry parameters and the conformational energy surfaces of meso or racemicdyad of poly(acrylic acid) (PAA) and poly(methacrylic acid) (PMAA). Three differentcarbonyl-bond orientations of side-groups resulted in the differences in depth of potentialwells in their energetic contours for a meso or a racemic dyad. These discrepancies areinterpreted as a result of various fine structures corresponding to grid search conformationsas well as thereby different interactions. The analysis on the most stable conformationsof PMAA confirmed that the ester groups are nearly perpendicular to the plane definedby the two adjacent skeletal bonds but may possibly change their relative orientations tomeet the requirement of lower energy during the conformational state transition. For eachpolyme, two global energy maps of a meso and a racemic dyad were finally constructedfrom the superposition of energy data for the three kinds of side-group orientations by theBoltzmann factors. From an ensemble average, the proposed scheme with three rotationalisomeric states (RIS) allowed us to access the experimentally unperturbed dimensions ofPAA chain via the configurational statistical mechanics. Although the calculation wasbased on the short-range, local interactions, it was interested to note that the experimentalcharacteristic ratios just fell within the range calculated for atactic chains.     

The theory of viscoelastic characteristics of a highly stretched macromolecule in single molecule AFM

The theory for the deformation of a model macromolecule stretched by its ends under the action of high constant and low periodic forces is constructed. The macromolecule is composed of monomer units in three conformational states. The proposed theory describes the regime of a severe stretching of a macromolecule extended to a length close to its contour length, when its extension proceeds via conformational transitions between different states of monomer units. The structural parameters of the monomer unit are found to correlate with viscoelastic characteristics, which are calculated from the experimental results on the deformation of an individual macromolecule obtained by the frequency atomic force microscopy. For a monomer unit with three conformations, the force dependences of viscoelastic characteristics (effective coefficients of elasticity and friction) can show one or two minima. When the experimental dependences of the above parameters show two minima, the monomer unit can have three or more equilibrium states. With the knowledge of the viscoelastic characteristics of a macromolecule, it is possible to unequivocally estimate all structural parameters of a monomer unit for its three-state conformational model. When the force dependence of viscoelastic characteristics show only one minimum, the monomer unit can have two or more states and analysis of the corresponding viscoelastic characteristics at the minimum makes it possible to select between two- and three-state conformational models. Then, for the three-state model, experimental data allow the prediction of only equilibrium parameters of the monomer unit (position of the minima and energy); dynamic parameters (positions and height of barriers between equilibrium states) remain indeterminate. The proposed theory is used for the interpretation of the viscoelastic characteristics of dextran obtained by single-molecule AFM experiments. The three-state conformational model of a dextran unit is shown to agree better with the experimental data than with the two-state conformational model.     

A new force field (ECEPP-05) for peptides, proteins, and organic molecules

Parametrization and testing of a new all-atom force field for organic molecules and peptides with fixed bond lengths and bond angles are described. The van der Waals parameters for both the organic molecules and the peptides were taken from J. Phys. Chem. B 2003, 107, 7143 and J. Phys. Chem. B 2004, 108, 12181. First, the values of the 1-4 nonbonded and electrostatic scale factors appropriate to the new force field were determined by computing the conformational energies of six model molecules, namely, ethanol, ethylamine, propanol, propylamine, 1,2-ethanediol, and 1,3-propanediol with different values of these factors. The partial atomic charges of these molecules were obtained by fitting to the electrostatic potentials calculated with the HF/6-31G quantum-mechanical method. Two different charge models (single- and multiple-conformation-derived) were also considered. We demonstrated that the charge model has a stronger effect on the conformational energies than the 1-4 scaling. The choice of a charge model affected the conformational energies of even the smallest molecules considered, whereas the effect of the 1-4 electrostatic or nonbonded scaling was apparent only for 1,3-propanediol. The best agreement with high-level ab initio data was obtained with the multiple-conformation-derived charges and with no scaling of the 1-4 nonbonded or electrostatic interactions (scale factors of 1.0). Next, the torsional parameters of a large number of neutral and charged organic molecules, assumed to be models of the side chains of the 20 naturally occurring amino acids, were computed by fitting to rotational energy profiles obtained from ab initio MP2/6-31G calculations. The quality of the fits was high with average errors for torsional profiles of less than 0.2 kcal/mol. To derive the torsional parameters for the peptide backbone, the partial atomic charges of the 20 neutral and charged amino acids were obtained by fitting to the electrostatic potentials of terminally blocked amino acids using the HF/6-31G quantum-mechanical method. Then, the phi-psi energy maps of Ac-Ala-NMe and Ac-Gly-NMe were computed using MP2/6-31G//HF/6-31G quantum-mechanical methods. The phi-psi energy map of Ac-Ala-NMe was used for refinement of the nonbonded parameters for the backbone nitrogen and hydrogen bonded to it. Subsequently, the main-chain torsional parameters were obtained by fitting the molecular mechanics energies to the phi-psi energy maps of Ac-Ala-NMe and Ac-Gly-NMe. The transferability of the entire force field was demonstrated by reproducing the main energy minima of terminally blocked Ala3 from the literature. The performance of the force field was also evaluated by simulating crystal structures of small peptides. By comparison of simulated and experimental data, examination of the torsional-angle and atom-positional root-mean-square deviations of the energy-minimized crystal structures from the corresponding X-ray model structures demonstrated high accuracy of the force field.     

Molecular modeling of polymers. 10. Characterization of conformational transitions of poly(acrylic acid) and poly(methacrylic acid) using dyad structures

The conformational profiles of nearest side-chain neighbors, methylene-dyad structures, of poly(acrylic acid), PAA, and poly(methacrylic acid), PMA, were determined as a function of tacticity, extent of ionization, and presence of counterion. The dominant backbone conformer states are quite similar for both isotactic and syndiotactic diads in a common charge state. Thus, the overall dimensional properties of isotactic syndiotactic and atactic chains of PAA or PMA, based upon dyad interactions, are predicted to be alike for a given charge state. Significant deviations from precise t, g⁺, and g^? states are found for the dyad minimum energy conformations. The rod-to-coil and coil-to-rod transitions observed in PAA and PMA, respectively, as a function of increasing counterion concentration can be explained, to a large extent, by the conformational profiles of the corresponding dyad model structures. © 1994 John Wiley & Sons, Inc.     

Pathways for conformational change in nitrogen regulatory protein C from discrete path sampling

Pathways corresponding to the conformational change in nitrogen regulatory protein C are calculated using the CHARMM19 force field with an implicit solvation model. Our analysis employs the discrete path sampling approach to grow a database of local minima and transition states from the potential energy surface that contains kinetically relevant pathways. The pathways with the largest contribution to the phenomenological two-state rate constants are found to exhibit a number of structural features that agree with experimental observations. Further details of the calculated pathways for conformational change may therefore provide useful predictions of how this large-scale motion is achieved.     

Analysis of anisotropy in dielectric absorption due to defects in the polyoxymethylene crystal

The dielectric absorption due to terminal polar groups localized in defect regions of polyoxymethylene crystals shows an anisotropy relative to an applied field. An attempt to interpret this anisotropy has been made by applying the barrier theory of Hoffman. The potential energy map for the rotation of the terminal polar group calculated from conformational analysis gives two minima. The angle between the dipole moment of the terminal OH and the fiber axis calculated in terms of the two conformations corresponding to the potential energy minima is in good agreement with results from infrared dichroism. This agreement is considered as evidence that the conformational analysis is reliable for estimating the potential energy minima required in the calculation according to the barrier theory. The barrier height obtained by the conformational analysis and the anisotropy calculated from the components of the dipole moments for the terminal polar group in terms of the barrier theory are in qualitative agreement with the experimental data.     

2D‐ and 3D‐ Potential Energy Surfaces of β‐(1→3)‐Linked Disaccharides Calculated with the MM3 Force‐Field

The adiabatic conformational surfaces of sixteen 4′,6′,6‐trideoxy‐β‐d‐(1→3)‐linked disaccharides were obtained using the MM3 force‐field. Calculations were carried out on disaccharides with different configurations at C2, C4 and C2′, which are neighbors to the glycosidic linkage, as well as that of the linked carbon (C3). The surfaces were plotted as contour maps and as 2D graphs representing the energy vs. the ψ angle. The resulting maps were similar in each case, indicating that the substituents do not play a major role in the conformational features of these disaccharides. However, the number of minima, the preferred minimum conformation and the flexibility depended on the configurations of the mentioned carbons. Vicinal equatorial substituents tend to decrease the overall flexibility, especially those on C2, although cross over effects were found. The relative stabilities of the minimal energy conformations of the 16 compounds were compared with those of their equivalent α‐linked counterparts. Deviations of the predicted increased stabilities of equatorially substituted compounds over axially substituted ones follow a relationship with their configurations, and consequently can serve to formulate predictive trends.     

Combined vibrational,conformational energy and electron diffraction studies of trans-2-decalone

The structure of trans-2-decalone was investigated by combined gas phase electron diffraction, conformational energy and vibrational analyses. In this study first the minimum energy conformations for trans-2-decalone were calculated by molecular mechanics techniques using a force field described in the literature; the same field and the minimum energy conformations were then used in subsequent vibrational analyses to calculate the mean amplitudes of vibration for each minimum energy conformation of trans-2-decalone; these mean amplitudes and the corresponding internuclear distances were then used to calculate theoretical electron diffraction radial distribution curves which were compared to the experimental curves. Four conformational energy minima were investigated with one or both rings in a chair or non-chair form. The results of the combined investigations indicate that the molecule exists in the conformation which has both rings in a distorted chair form.     

In defense of adiabatic ϕ/ψ mapping for cellobiose and other disaccharides

Thorough conformational study of cellobiose requires consideration of numerous arrangements of the exocyclic groups. Therefore, it is customary to prepare a number of structures with different arrangements of hydroxyl and hydroxymethyl groups. These “starting geometries” are then given different values of the glycosidic linkage torsion angles ϕ and ψ. At each increment of ϕ and ψ, the energy is calculated. Usually, the final product is an “adiabatic” contour plot of the lowest energy at each ϕ/ψ point after considering all of the starting geometries. The present paper advocates for adiabatic maps despite the statement by Schnupf and Momany (preceding paper) that adiabatic maps are not of interest because they contain sparse details about the structures at each minimum. Similar information is computed by their method and adiabatic mapping, and comparable details can be provided from adiabatic studies. Although Schnupf and Momany presented maps from calculations in vacuum and in water that considered all of their calculated energies, they favored the presentation of two to four maps for each of 36 individual minima, each with its own zero of relative energy. However, previous work showed that more structures are needed to provide the lowest energies at each point in ϕ/ψ space. Following their preferred strategy would result in even more maps when the added structures are considered. The need to map individual minima can be avoided by starting calculations with the same exocyclic orientations at each ϕ/ψ point instead of using the preceding optimized structure to start the next energy minimization. Using the same orientations at each point allows periodic maps that depict barriers between minima.     

Beiträge zur Chemie der Pyrrolpigmente, 81. Mitt.: Kraftfeldrechnungen an Gallenfarbstoffen: Die Energiehyperfläche von 2,3-Dihydrobilin-1,19-dionen

Summary The energy hypersurface of 2,3-dihydrobilin-1,19-diones is analyzed with respect to their conformational aspects using a specialized force field. Estimations of helix interconversion energies, chiral discrimination, geometries of global minima, and relative energies and geometries of diastereomeres compare favourably with available experimental data from the literature.

     

Quantum mechanical calculations of tryptophan and comparison with conformations in native proteins

We report a detailed analysis of the potential energy surface of N-acetyl-l-tryptophan-N-methylamide, (NATMA) both in the gas phase and in solution. The minima are identified using the density-functional-theory (DFT) with the 6-31g(d) basis set. The full potential energy surface in terms of torsional angles is spanned starting from various initial configurations. We were able to locate 77 distinct L-minima. The calculated energy maps correspond to the intrinsic conformational propensities of the individual NATMA molecule. We show that these conformations are essentially similar to the conformations of tryptophan in native proteins. For this reason, we compare the results of DFT calculations in the gas and solution phases with native state conformations of tryptophan obtained from a protein library. In native proteins, tryptophan conformations have strong preferences for the beta sheet, right-handed helix, tight turn, and bridge structures. The conformations calculated by DFT, the solution-phase results in particular, for the single tryptophan residue are in agreement with native state values obtained from the Protein Data Bank.     

聚合物链构象的研究 II: 1,2-聚丁二烯的构象特征和链分子的特征比

基于Flory的链分子统计理论, 用MM2分子力学程序改进了1,2-聚丁二烯构象分析,同时讨论了温度的影响. 着重考查了全同1,2-聚丁二烯特征比随能量的变化规律, 并且注意到聚苯乙烯, 聚丙烯酸甲酯等全同链的特征比按相似规律变化, 从而表现了聚烯烃全同链的共同特征.     

Harmonic dynamics of beta-D-fructopyranose

The vibrational spectra of beta-D-fructopyranose crystals have been recorded in the 4000-400 cm(-1) region using the infrared and in the 4000-20 cm(-1) region using the Raman. These spectra are used as an experimental basis in order to establish a force field for the beta-D-fructopyranose molecule in the crystalline state through a normal co-ordinates analysis. For this purpose, a modified Urey-Bradley-Shimanoushi force field was combined with an intermolecular potential energy function that includes the van-der-Walls interactions, the electrostatic terms, and an explicit hydrogen bond function. The force field parameters are derived from those of beta-D-glucose and are fitted so as to obtain a good agreement between the calculated and the observed frequencies. The results obtained demonstrate the reliability and the transferability of the set of parameters constituting the initial force field. The fitted force field reproduces the experimental spectra to a marked degree of accuracy.     

Conformational analysis and kinetics of ring inversion for methylene- and dimethylsilyl-bridged dicyclooctatetraene

Dicyclooctatetraenylmethane (1) and dicyclooctatetraenyldimethylsilane (2) in THF-d(8) at 272 K exist as mixtures of diastereomers in ratios of 1:0.8 and 1:1, respectively. Nine energy minima (four meso and five racemic conformers) were located for each compound by geometry optimization at the HF/6-31G level of theory. The effects of torsional strain, steric interactions and dynamic electron correlation were analyzed. The diastereomeric ratios for 1 and 2 were reproduced reasonably well from the total energy calculated for each conformer corrected for its conformational enthalpy and entropy contributions. The ratio of rate constants for bond shift (BS) (k(BS)(1)/k(BS)(2)) is three times greater than the corresponding ratio for ring inversion. This suggests that additional substituent effects, such as pi interactions, are operative in the transition state for BS.     

Conformational analysis of some ortho-hydroxyazoic dyes by the PCILO method

The quantum mechanical MO method PCILO is used to perform a detailed conformational analysis of ortho-hydroxyazobenzene and 1-phenyl azo 2-napthol. Several energy minima are obtained for each compound, after a simultaneous optimization of the main geometric parameters. Comparison is made with the corresponding para compounds. The calculated results are discussed in relation to the available experimental data.     

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.     

The COMPASS force field: parameterization and validation for phosphazenes

A new, condensed-phase optimised ab-initio force field, COMPASS, has been developed recently. In this paper, the validation of COMPASS for phosphazenes is presented. The functional forms of this force field are of the consistent force field (CFF) type. Charges and bonded terms were derived from HF/6–31G1 calculations, while the nonbonded parameters (L-J 9-6 vdW potential) were initially transferred from the polymer consistent force field, pcff, and optimised using MD simulations of condensed-phase properties. As a validation of COMPASS, molecular mechanics calculations and molecular dynamics simulations have been made on a number of isolated molecules, liquids, and crystals. The calculated molecular structure, vibration frequencies, conformational properties for isolated molecules, crystal cell parameters and density, liquid density, and heat of evaporation agreed favourably with most experimental data. The special conformational properties of the tetracyclophosphazenes, (NPCI₂)₄ and (NPF₂)₄, in the solid state are discussed based on molecular mechanics and CASTEP ab-initio calculations. The effect of nonbonded cutoff distance and different algorithms for pressure control in NPT simulation was also investigated. Finally, molecular dynamics using the COMPASS force field was used to predict properties of three isomers of high-molecular-weight amorphous poly(dibutoxyphosphazenes). In this case, excellent agreement was achieved between densities and glass transition temperatures obtained from dynamics and experimental data.     

Parameterization and validation of Gromos force field to use in conformational analysis of epoxidic systems

In order to study the conformational space of new natural products derivatives using molecular mechanics (MM) and molecular dynamics (MD), the Gromos force field has been expanded to include epoxidic systems. The parameterization and validation of Gromos were done to simulate 22, 23 epoxides in brassinosteroids analogs. The parameters were derived with an emphasis on the dependence between energy and dihedral angle due to its relevance in the conformational analysis. Molecular dynamics simulations of two model systems similar to those of interest were performed to validate the force field with the proposed parameters. Excellent agreement has been obtained between the MD simulation and the results of a potential energy surface (PES) calculated at B3LYP/6-31G^** level.     

Simulation of multiphase systems utilizing independent force fields to control intraphase and interphase behavior

Fixed‐charge empirical force fields have been developed and widely used over the past three decades for all‐atom molecular simulations. Most simulation programs providing these methods enable only one set of force field parameters to be used for the entire system. Whereas this is generally suitable for single‐phase systems, the molecular environment at the interface between two phases may be sufficiently different from the individual phases to require a different set of parameters to be used to accurately represent the system. Recently published simulations of peptide adsorption to material surfaces using the CHARMM force field have clearly demonstrated this issue by revealing that calculated values of adsorption free energy substantially differ from experimental results. Whereas nonbonded parameters could be adjusted to correct this problem, this cannot be done without also altering the conformational behavior of the peptide in solution, for which CHARMM has been carefully tuned. We have developed a dual‐force‐field approach (Dual‐FF) to address this problem and implemented it in the CHARMM simulation package. This Dual‐FF method provides the capability to use two separate sets of nonbonded force field parameters within the same simulation: one set to represent intraphase interactions and a separate set to represent interphase interactions. Using this approach, we show that interfacial parameters can be adjusted to correct errors in peptide adsorption free energy without altering peptide conformational behavior in solution. This program thus provides the capability to enable both intraphase and interphase molecular behavior to be accurately and efficiently modeled in the same simulation. © 2012 Wiley Periodicals, Inc.