Structure of dicyano-pyridinium methylide and amidocyano-pyridinium methylide using ab initio and semi-empirical methods

Taking into account the X-ray diffraction patterns of dicyano-pyridinium methylide and amidocyano-pyridinium methylide, comparative ab initio and semi-empirical studies have been performed. The aim of this study is to elucidate some electronic and structural properties of the cycloimmonium ylides. In fact, we found that the positive charge of the ylide nitrogen atom is delocalized on the pyridine ring. The ylide carbon atom is found to be insignificantly charged. This proves that the formal negative charge often accepted for the ylidic carbanion is delocalized. Thus, we demonstrate the existence of the resonance interaction between the ylidic carbanion and the positive aromatic ring as a factor of stability for planar cycloimmonium ylides. The negative charges found for the cyclic carbon atoms adjacent to the ylide nitrogen atom precludes any nucleophilic addition on the α carbon atoms in the heterocyclic ring. This is in good agreement with the experiments, where no nucleophilic addition on such atoms has ever been observed. Among the six semi-empirical methods used in this paper, the AM1 method is the most appropriate in the study of planar cycloimmonium ylides. This method is found to reproduce the experimental values and ab initio results with good accuracy.     

Development of an internal searching algorithm for parameterization of the MM2/MM3 force fields

Application of Allinger's MM2/MM3 force fields to molecules of real interest is frequently hindered by the lack of parameters for various heterocyclic systems and for poly-functionalized molecules. A common approach to this problem is to manually choose missing parameters “by analogy” with those that are part of the force field's internal parameter set. Naturally, this is generally attempted only by those possessing extensive experience with force fields. In order to use the MM2/MM3 force fields to study herbicides, an algorithm has been developed to automate this process for the non MM2 specialist. Using a set of “relative cost” criteria for atom type replacement, the algorithm searches the force field parameter set and selects the most appropriate parameters for a given molecule whose MM2 output file contains “missing parameter” errors. The program selects parameter error messages from a standard MM2 output file, finds analogous parameters, asks the user to verify their appropriateness and creates a standard MM2 parameter deck for the molecule of interest.     

Alcohols,ethers, carbohydrates,and related compounds. II. The anomeric effect

The anomeric effect has been studied for a variety of compounds using the MM4 force field, and also using MP2/6-311++G(2d,2p) ab initio calculations and experimental data for reference purposes. Geometries and energies, including conformational, rotational barriers, and heats of formation were examined. Overall, the agreement of MM4 with the experimental and ab initio data is good, and significantly better than the agreement obtained with the MM3 force field. The anomeric effect is represented in MM4 by various explicit terms in the force constant matrix. The bond length changes are accounted for with torsion-stretch elements. The angle changes are accounted for with torsion-bend elements. The energies are taken into account with a number of torsional terms in the usual way. A torsion-torsion interaction is also of some importance. With all of these elements included in the calculation, the MM4 results now appear to be adequately accurate. The heats of formation were examined for a total of 12 anomeric compounds, and the experimental values were fit by MM4 with an RMS error of 0.42 kcal/mol.     

Molecular mechanics (MM3) calculations on lithium amide compounds

The MM3 force field has been extended to deal with the lithium amide molecules that are widely used as efficient catalysts for stereoselective asymmetric synthesis. The MM3 force field parameters have been determined on the basis of the ab initio MP2/6-31G* and/or DFT (B3LYP/6-31G*, B3-PW91/6-31G*) geometry optimization calculations. To evaluate the electronic interactions specific to the lithium amides derived from the diamine molecules properly, the Lewis bonding potential term for the interaction between the lithium atom and the nonbonded adjacent electronegative atom such as nitrogen was introduced into the MM3 force field. The bond dipoles were evaluated correctly from the electronic charges on the atoms calculated by fitting to the electrostatic potential at points selected. The MM3 results on the molecular structures, conformational energies, and vibrational spectra show good agreement with those from the quantum mechanical calculations.     

On the effect of a variation of the force field, spatial boundary condition and size of the QM region in QM/MM MD simulations

During the past years, the use of combined quantum-classical, QM/MM, methods for the study of complex biomolecular processes, such as enzymatic reactions and photocycles, has increased considerably. The quality of the results obtained from QM/MM calculations is largely dependent on five aspects to be considered when setting up a molecular model: the QM Hamiltonian, the MM Hamiltonian or force field, the boundary and coupling between the QM and MM regions, the size of the QM region and the boundary condition for the MM region. In this study, we systematically investigate the influence of a variation of the molecular mechanics force field and the size of the QM region in QM/MM MD simulations on properties of the photoactive part of the blue light photoreceptor protein AppA. For comparison, we additionally performed classical MD simulations and studied the effect of a variation of the type of spatial boundary condition. The classical boundary conditions and the force field used in a QM/MM MD simulation are shown to have non-neglegible effects upon the structural and energetic properties of the protein which makes it advisable to minimize computational artifacts in QM/MM MD simulations by application of periodic boundary conditions and a thermodynamically calibrated force field. A comparison of the structural and energetic properties of MD simulations starting from two alternative, different X-ray structures for the blue light utilizing flavin protein in its dark state indicates a slight preference of the two force fields used for the so-called Anderson structure over the Jung structure.     

分子力场进展

分子力学（简称ＭＭ）是近年来化学家常用的一种计算方法。与量子力学从头计算和半经验方法相比，用分子力学处理大分子可以大大节省计算时间，而且，在大多数情况下，用分子力学方法计算得到的分子几何构型参数与实验值之间的差值可在实验误差范围之内。所以，分子力学是研究生物化学体系的有效和可行的手段。分子力学的核心是分子力场。本文介绍了分子力场的量子力学背景、分子力场和光谱力场之间的关系。分子力场的一般形式、分力     

Strain energies of some bridgehead olefins as calculated with the MM2 force field

The MM 2 force field has been used to calculate the strain energies of a representative series of bridgehead alkenes, and the results compared to similar previous calculations using the MM 1 force field. The new results roughly parallel the old ones, although the strain energy of a given compound is normally higher with MM 2 than MM 1. These differences are largely negated, however, when the OS (olefinic strain) value is considered.     

Etude des reactions des diazoderives avec les cycloimmonium ylures-I : Action des sels de diazonium sur quelques pyridinium - ylures

The synthesis of cycloimmonium salts of the type $\text{7}$, $\text{8}$ and the corresponding cycloimmonium ylides $\text{9}$, $\text{10}$ are reported. In the reaction with diazonium salts $\text{11}$, $\text{12}$ the pyridinium monosubstituted carbanion ylides $\text{9}$, $\text{10}$ give the pyridinium disubstituted carbanion ylides $\text{17}$ – $\text{20}$. These are new types of isolable stable ylides. The synthesis involves the formation “in situ” of ylides $\text{9}$, $\text{10}$ which are bonded by their nucleophile ylide carbon atom to the nitrogen atom in diazonium salts. The intermediat formation of cycloimmonium salts $\text{13}$ – $\text{16}$ must be accepted. The structures of all compounds presented in this paper have been established by using elementary analysis, IR and ¹H-RMN spectra.     

Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions. II. An energy decomposition analysis

QM/MM methods have been developed as a computationally feasible solution to QM simulation of chemical processes, such as enzyme-catalyzed reactions, within a more approximate MM representation of the condensed-phase environment. However, there has been no independent method for checking the quality of this representation, especially for highly nonisotropic protein environments such as those surrounding enzyme active sites. Hence, the validity of QM/MM methods is largely untested. Here we use the possibility of performing all-QM calculations at the semiempirical PM3 level with a linear-scaling method (MOZYME) to assess the performance of a QM/MM method (PM3/AMBER94 force field). Using two model pathways for the hydride-ion transfer reaction of the enzyme dihydrofolate reductase studied previously (Titmuss et al., Chem Phys Lett 2000, 320, 169-176), we have analyzed the reaction energy contributions (QM, QM/MM, and MM) from the QM/MM results and compared them with analogous-region components calculated via an energy partitioning scheme implemented into MOZYME. This analysis further divided the MOZYME components into Coulomb, resonance and exchange energy terms. For the model in which the MM coordinates are kept fixed during the reaction, we find that the MOZYME and QM/MM total energy profiles agree very well, but that there are significant differences in the energy components. Most significantly there is a large change (approximately 16 kcal/mol) in the MOZYME MM component due to polarization of the MM region surrounding the active site, and which arises mostly from MM atoms close to (<10 A) the active-site QM region, which is not modelled explicitly by our QM/MM method. However, for the model where the MM coordinates are allowed to vary during the reaction, we find large differences in the MOZYME and QM/MM total energy profiles, with a discrepancy of 52 kcal/mol between the relative reaction (product-reactant) energies. This is largely due to a difference in the MM energies of 58 kcal/mol, of which we can attribute approximately 40 kcal/mol to geometry effects in the MM region and the remainder, as before, to MM region polarization. Contrary to the fixed-geometry model, there is no correlation of the MM energy changes with distance from the QM region, nor are they contributed by only a few residues. Overall, the results suggest that merely extending the size of the QM region in the QM/MM calculation is not a universal solution to the MOZYME- and QM/MM-method differences. They also suggest that attaching physical significance to MOZYME Coulomb, resonance and exchange components is problematic. Although we conclude that it would be possible to reparameterize the QM/MM force field to reproduce MOZYME energies, a better way to account for both the effects of the protein environment and known deficiencies in semiempirical methods would be to parameterize the force field based on data from DFT or ab initio QM linear-scaling calculations. Such a force field could be used efficiently in MD simulations to calculate free energies.     

Three‐electron two‐center bonding in cycloimmonium ylides

We explore the possibility that a 3‐electron‐2‐center bonding exists in cycloimmonium ylides. To detect this bonding in a polyatomic system, 3‐electron‐1‐hole density operators, characterizing a Pauling 3‐electron bond, are used in the framework of second quantization formalism. The weights of 3‐electron resonance structures are calculated and compared with the weights of 2‐electron structures for the ylide bond of pyridinium dicyanomethylide; the correlations of (↑↓) and (↑) electronic events, involved in the 3‐electron resonance structures, are also investigated. The calculations are performed in various approximation levels, and both orthogonal and nonorthogonal natural atomic orbitals are adopted. All calculations show that a 3‐electron bond exists between N and C atoms of ylide bond, but this bonding is not extended in C atoms of the pyridinium group. The interactions of α,β electrons (at the configuration interaction [CI] level) increase the localization of electrons, the weights of 3‐electron resonance structures, and thus the probability for 3‐electron bonding. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Modeling the stereoselectivity of the beta-amino alcohol-promoted addition of dialkylzinc to aldehydes

The title reaction has been modeled by a Q2MM force field, allowing for rapid evaluation of several thousand TS conformations. For 10 experimental systems taken from the literature, the pathway leading to the major enantiomer has been identified. Furthermore, several possible contributions to the minor enantiomer have been investigated, providing an identification of the reasons for the sometimes moderate enantioselectivity of the title reaction, and allowing for future rational improvement of existing ligands. The favored pathways to the minor enantiomer, which must be blocked for significant selectivity improvement, differ strongly among ligands. Thus, design ideas are not necessarily transferable between ligand classes, but must be developed for each reaction on the basis of the pathway that needs to be blocked in each specific case. However, we have identified some general structure-selectivity relationships.     

A molecular mechanics study of the Si?O bond and alkyl-silanes

The standard MM2 force field and program have been modified to include Si? O groups, the force constants being derived from ab initio wavefunctions, and using partial atomic charges calculated from the empirical algorithm CHARGE2. Molecular mechanics calculations have been carried out on disiloxane, dimethoxy-dimethylsilane, methyl silyl ether, and cyclotrisiloxane, and reasonable agreement has been obtained between the observed and calculated geometries. In addition, the energies obtained using the modified force field have been tested against experimental data on alkyl silanes where energetic and structural information is available. Again good agreement is obtained. The application of the force field to extended Si? O systems will also be discussed.     

Parameter analysis and refinement toolkit system and its application in MM3 parameterization for phosphine and its derivatives

The multiparameter multistep relaxation (MPMSR) method, a routine within a new suite of parameterization programs entitled parameter analysis and refinement toolkit system (PARTS), was developed to assist in the development of molecular mechanics (MM3 and MM2) force field parameters and represents an ongoing effort in our laboratories to generate more accurate force fields in shorter times. In contrast to other computerized parameterization approaches, this method simulates intuition guided trial-and-error and has been used successfully within our laboratories to develop MM2 and MM3 force fields. The primary aim of this approach is to minimize human inspection time and effort, with simultaneous improvement in the efficiency and accuracy of the parameterization process. In an effort to validate the generality of the MPMSR method, a well parameterized data set of phosphine derivatives was reexamined. With the identical set of training molecules used in the original MM3 phosphine parameterization and with minimal human intervention, MPMSR shortened the process from several months to approximately five days. Although the previous phosphine force field is well parameterized, the newly generated MPMSR set of parameters has achieved an overall better fit to the experimentally observed data and ab initio calculations. © 1996 by John Wiley & Sons, Inc.     

A molecular mechanics (MM3) study of fluorinated hydrocarbons

A molecular mechanics study of small saturated hydrocarbons (up to C-6), substituted by up to six fluorines was carried out with the MM3 force field. Perfluorobutane and Teflon were also studied. A parameter set was developed for use in the calculation of bond lengths, bond angles, torsion angles, conformational energies, barriers to rotation, dipole moments, moments of inertia and vibrational frequencies for these compounds. The results are in good agreement with experiment when only one or two fluorines are present, but some rather large discrepancies were noted when the F/H ratio becomes high. These can be taken into account only by using a force field more complicated than MM3. Some of the requirements of such a force field are delineated. Some pertinent ab initio results are also reported in this article.     

Optimization of a molecular mechanics force field for type-II polyoxometalates focussing on electrostatic interactions: a case study

In this study, we have focussed on type-II polyanions such as [M(7)O(24)](6-), and we have developed and validated optimized force fields that include electrostatic and van der Waals interactions. These contributions to the total steric energy are described by the nonbonded term, which encompasses all interactions between atoms that are not transmitted through the bonds. A first validation of a stochastic technique based on genetic algorithms was previously made for the optimization of force fields dedicated to type-I polyoxometalates. To describe the new nonbonded term added in the functional, a fixed-charged model was chosen. Therefore, one of the main issues was to analyze that which partial atomic charges could be reliably used to describe these interactions in such inorganic compounds. Based on several computational strategies, molecular mechanics (MM) force field parameters were optimized using different types of atomic charges. Moreover, the influence of the electrostatic and van der Waals buffering constants and 1,4-interactions scaling factors used in the force field were also tested, either being optimized as well or fixed with respect to the values of CHARMM force field. Results show that some atomic charges are not well adapted to CHARMM parameters and lead to unrealistic MM-optimized structures or a MM divergence. As a result, a new scaling factor has been optimized for Quantum Theory of Atoms in Molecules charges and charges derived from the electrostatic potential such as ChelpG. The force fields optimized can be mixed with the CHARMM force field, without changing it, to study for the first time hepta-anions interacting with organic molecules.     

A force field for allenes and for nonlinear acetylenes within the MM2 approximation

Geometries and heats of formation for allenes may now be calculated with an extended version of MM2. The torsional barriers about bonds in an acetylenic unit are much more complicated than originally thought, if the unit is nonlinear. Ab initio calculations have been used to show just what these torsional barriers are, and the MM2 force field has been adapted to this information.