Showing papers in "Journal of Computational Chemistry in 2001"
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TL;DR: The “Activation‐strain TS interaction” (ATS) model of chemical reactivity is reviewed as a conceptual framework for understanding how activation barriers of various types of reaction mechanisms arise and how they may be controlled, for example, in organic chemistry or homogeneous catalysis.
Abstract: We present the theoretical and technical foundations of the Amsterdam Density Functional (ADF) program with a survey of the characteristics of the code (numerical integration, density fitting for the Coulomb potential, and STO basis functions). Recent developments enhance the efficiency of ADF (e.g., parallelization, near order-N scaling, QM/MM) and its functionality (e.g., NMR chemical shifts, COSMO solvent effects, ZORA relativistic method, excitation energies, frequency-dependent (hyper)polarizabilities, atomic VDD charges). In the Applications section we discuss the physical model of the electronic structure and the chemical bond, i.e., the Kohn–Sham molecular orbital (MO) theory, and illustrate the power of the Kohn–Sham MO model in conjunction with the ADF-typical fragment approach to quantitatively understand and predict chemical phenomena. We review the “Activation-strain TS interaction” (ATS) model of chemical reactivity as a conceptual framework for understanding how activation barriers of various types of (competing) reaction mechanisms arise and how they may be controlled, for example, in organic chemistry or homogeneous catalysis. Finally, we include a brief discussion of exemplary applications in the field of biochemistry (structure and bonding of DNA) and of time-dependent density functional theory (TDDFT) to indicate how this development further reinforces the ADF tools for the analysis of chemical phenomena. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 931–967, 2001
8,490 citations
TL;DR: Medium basis sets based upon contractions of Gaussian primitives are developed for the third‐row elements Ga through Kr, and good agreement with bond lengths and angles for representative vapor‐phase metal complexes is shown.
Abstract: Medium basis sets based upon contractions of Gaussian primitives are developed for the third-row elements Ga through Kr. The basis functions generalize the 6-31G and 6-31G* sets commonly used for atoms up to Ar. A reexamination of the 6-31G* basis set for K and Ca developed earlier leads to the inclusion of 3d orbitals into the valence space for these atoms. Now the 6-31G basis for the whole third-row K through Kr has six primitive Gaussians for 1s, 2s, 2p, 3s, and 3p orbitals, and a split-valence pair of three and one primitives for valence orbitals, which are 4s, 4p, and 3d. The nature of the polarization functions for third-row atoms is reexamined as well. The polarization functions for K, Ca, and Ga through Kr are single set of Cartesian d-type primitives. The polarization functions for transition metals are defined to be a single 7f set of uncontracted primitives. Comparison with experimental data shows good agreement with bond lengths and angles for representative vapor-phase metal complexes. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 976–984, 2001
1,788 citations
TL;DR: Vyazovkin et al. as discussed by the authors used an integration technique that properly accounts for the variation in the activation energy, which was implemented as a modification of the earlier proposed advanced isoconversional method and applied to the thermal decomposition of calcium oxalate monohydrate and ammonium nitrate.
Abstract: Integral isoconversional methods may give rise to noticeable systematic error in the activation energy when the latter strongly varies with the extent of conversion. This error is eliminated by using an integration technique that properly accounts for the variation in the activation energy. The technique is implemented as a modification of the earlier proposed advanced isoconversional method [Vyazovkin, S. J Comput Chem 1997, 18, 393]. The applications of the modified method are illustrated by simulations as well as by processing of data on the thermal decomposition of calcium oxalate monohydrate and ammonium nitrate. © 2000 John Wiley & Sons, Inc. J Comput Chem 22: 178–183, 2001
917 citations
TL;DR: The GROMOS96 45A3 parameter set should be suitable for application to lipid aggregates such as membranes and micelles, for mixed systems of aliphatics with or without water, for polymers, and other apolar systems that may interact with different biomolecules.
Abstract: Over the past 4 years the GROMOS96 force field has been successfully used in biomolecular simulations, for example in peptide folding studies and detailed protein investigations, but no applications to lipid systems have been published yet. Here we provide a detailed investigation of aliphatic liquid systems. For liquids of larger aliphatic chains, n-heptane and longer, the standard GROMOS96 parameter sets 43A1 and 43A2 yield a too low pressure at the experimental density. Therefore, a reparametrization of the GROMOS96 force field regarding aliphatic carbons was initiated. The new force field parameter set 45A3 shows considerable improvements for n-alkanes, cyclo-, iso-, and neoalkanes and other branched aliphatics. Liquid densities and heat of vaporization are reproduced for almost all of these molecules. Excellent agreement is found with experiment for the free energy of hydration for alkanes. The GROMOS96 45A3 parameter set should, therefore, be suitable for application to lipid aggregates such as membranes and micelles, for mixed systems of aliphatics with or without water, for polymers, and other apolar systems that may interact with different biomolecules. c
856 citations
TL;DR: In this paper, an alternative method, M-SHAKE, which solves the coupled equations simultaneously by matrix inversion, was proposed and compared in simulations of the pure solvents water, dimethyl sulfoxide, and chloroform.
Abstract: A common method for the application of distance constraints in molecular simulations employing Cartesian coordinates is the SHAKE procedure for determining the Lagrange multipliers regarding the constraints. This method relies on the linearization and decoupling of the equations governing the atomic coordinate resetting corresponding to each constraint in a molecule, and is thus iterative. In the present study, we consider an alternative method, M-SHAKE, which solves the coupled equations simultaneously by matrix inversion. The performances of the two methods are compared in simulations of the pure solvents water, dimethyl sulfoxide, and chloroform. It is concluded that M-SHAKE is significantly faster than SHAKE when either (1) the molecules contain few distance constraints (solvent), or (2) when a high level of accuracy is required in the application of the constraints. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 501–508, 2001
849 citations
TL;DR: A very powerful and efficient computational approach to solve the exchange problem in high nuclearity spin clusters with all kind of exchange interactions (isotropic and anisotropic), including the single-ion anisotrop effects.
Abstract: M agnetic molecular clusters, i.e., molecular assemblies formed by a finite number of exchange-coupled magnetic moments, are currently receiving much attention in several active areas of research as molecular chemistry, magnetism, and biochemistry. A reason for this interest lies in the possibility to use simple molecular clusters as magnets of nanometer size exhibiting unusual magnetic properties as superparamagnetic like behavior or quantum tunneling of magnetization.2 – 4 Organic molecules of increasing sizes and large number of unpaired electrons are being explored as a means of obtaining building blocks for molecule-based magnets.5 Magnetic clusters of metal ions are also relevant in biochemistry.6 This area between molecule and bulk will require new theoretical concepts and techniques for investigation of their peculiar properties. Still, the theoretical treatment required to understand the magnetic and spectroscopic properties of this wide variety of compounds is a challenging problem in molecular magnetism.7 For a long time, this problem has been mostly restricted to treat comparatively simple clusters comprising a reduced number of exchange-coupled centers and special spin topologies, for which solutions can be obtained either analytically or numerically. However, on increasing the spin nuclearity of the cluster, the problem rapidly becomes unapproachable because the lack of translational symmetry in the clusters. An additional complication is the spin anisotropy of the cluster. Until now only the isotropic-exchange case has been treated, so as to take full advantage of the spin symmetry of the cluster.8 In this article we present a very powerful and efficient computational approach to solve the exchange problem in high nuclearity spin clusters with all kind of exchange interactions (isotropic and anisotropic), including the single-ion anisotropic effects. The clusters are formed by an arbitrary number of exchangecoupled centers that combine different spin values and arbitrary topology. This approach is based on the use of the irreducible tensor operators (ITO) technique.7, 9 – 12 It allows evaluation of both eigenvalues and eigenvectors of the system, and then, calculation of the magnetic susceptibility, magnetization, or heat capacity, and also the inelastic neutron scattering spectra. In the following sections we will present both the theory and the four different implemented FORTRAN programs that integrate a package called MAGPACK . In the last section some examples are presented in order to show the possibilities of the programs.
744 citations
TL;DR: Nonbonded and torsional parameters for carboxylate esters, nitriles, and nitro compounds have been developed for the OPLS‐AA force field and are in excellent agreement with experimental values.
Abstract: Nonbonded and torsional parameters for carboxylate esters, nitriles, and nitro compounds have been developed for the OPLS‐AA force field. In addition, torsional parameters for alkanes have been updated. These parameters were fit to reproduce ab initio gas‐phase structures and conformational energetics, experimental condensed‐phase structural and thermodynamic properties, and experimental free energies of hydration. The computed densities, heats of vaporization, and heat capacities for fifteen liquids are in excellent agreement with experimental values. The new parameters permit accurate molecular modeling of compounds containing a wider variety of functional groups, which are common in organic molecules and drugs. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1340–1352, 2001
441 citations
TL;DR: In this article, a methodology to derive RESP charges for molecular mechanical models that include "lone pairs" on lone-pair donor sites and atom-centered polarizabilities was developed.
Abstract: We have developed a methodology to derive RESP charges for molecular mechanical models that include “lone pairs” on lone-pair donor sites and atom-centered polarizabilities. This approach uses a very high level ab initio cc-pVTZ basis set,1 where the multipole moments of the molecules are as accurate as possible. The partial charges are derived self-consistently so that the model, whose electrostatic potential comes from both partial charges and induced dipoles, reproduces the quantum mechanical electrostatic potential. We then study the ability of such models to reproduce the aqueous solvation free energy of methanol and N-methyl acetamide (NMA), the base pair hydrogen bonding of the 26 base pairs analyzed by Hobza et al. and the chloroform/water partition coefficients of the five N-methyl substituted nucleic acid bases. The base pair H-bond energies are described as well as the atom centered additive model, after modifying the van der Waals parameter on the NH to give reasonable base pair H-bond distances. The experimental solvation free energies (gas→water) of methanol and NMA are well described, and the water/CHCl3 partition coefficients are improved over the additive model, without any parameter changes. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1048–1057, 2001
363 citations
TL;DR: This work introduces a continuous smooth permittivity function into Poisson–Boltzmann techniques for continuum approaches to modeling the solvation of small molecules and proteins using a Gaussian method to describe volume exclusion.
Abstract: This work introduces a continuous smooth permittivity function into Poisson–Boltzmann techniques for continuum approaches to modeling the solvation of small molecules and proteins. The permittivity function is derived using a Gaussian method to describe volume exclusion. The new method allows a rigorous determination of solvent forces within a grid-based technology. The generality of approach is demonstrated by considering a range of applications for small molecules and macromolecules. We also present a very complete statistical analysis of grid errors, and show that the accuracy of our Gaussian-based method is improved over standard techniques. The method has been implemented in a new code called ZAP, which is freely available to academic institutions.1 © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 608–640, 2001
337 citations
TL;DR: In this article, a new charge analysis is presented that gives an accurate description of the electrostatic potential from the charge distribution in molecules, which is achieved in three steps: first, the total density is written as a sum of atomic densities; next, a set of atomic multipoles are defined; finally, these atomic multipole are reconstructed exactly by distributing charges over all atoms.
Abstract: A new charge analysis is presented that gives an accurate description of the electrostatic potential from the charge distribution in molecules. This is achieved in three steps: first, the total density is written as a sum of atomic densities; next, from these atomic densities a set of atomic multipoles is defined; finally, these atomic multipoles are reconstructed exactly by distributing charges over all atoms. The method is generally applicable to any method able to provide atomic multipole moments, but in this article we take advantage of the way the electrostatic potential is calculated within the Density Functional Theory framework. We investigated a set of 31 molecules as well as all amino acid residues to test the quality of the method, and found accurate results for the molecular multipole moments directly from the DFT calculations. The deviations from experimental values for the dipole/quadrupole moments are also small. Finally, our Multipole Derived Charges reproduce both the atomic and molecular multipole moments exactly. c 2000 John Wiley & Sons, Inc. J Comput Chem 22: 79-88, 2001
168 citations
TL;DR: Results are presented from a charge derivation protocol that determines the partial charges by averaging charges computed for conformations selected from explicitly solvated MD simulations, performed under periodic boundary conditions.
Abstract: In the calculation of partial atomic charges, for use in molecular mechanics or dynamics simulations, it is common practice to select only a single conformation for the molecule of interest. For molecules that contain rotatable bonds, it is preferable to compute the charges from several relevant conformations. We present here results from a charge derivation protocol that determines the partial charges by averaging charges computed for conformations selected from explicitly solvated MD simulations, performed under periodic boundary conditions. This approach leads to partial charges that are weighted by a realistic population of conformations and that are suitable for condensed phase simulations. This protocol can, in principle, be applied to any class of molecule and to nonaqueous solvation. Carbohydrates contain numerous hydroxyl groups that exist in an ensemble of orientations in solution, and in this report we apply ensemble averaging to a series of methyl glycosides. We report the extent to which ensemble averaging leads to charge convergence among the various monosaccharides and among the constituent atoms within a given monosaccharide. Due to the large number of conformations (200) in our ensembles, we are able to compute statistically relevant standard deviations for the partial charges. An analysis of the standard deviations allows us to assess the extent to which equivalent atom types may, nevertheless, require unique partial charges. The configurations of the hydroxyl groups exert considerable influence on internal energies, and the limits of ensemble averaged charges are discussed in terms of these properties.
TL;DR: The final MST model is able to reproduce the experimental free energy of solvation for 62 compounds and the octanol/water partition coefficient (log Pow) for 75 compounds with a root‐mean‐square deviation of 0.6 kcal/mol and 0.4 (in units of log’P), respectively.
Abstract: This study reports the parametrization of the HF/6‐31G(d) version of the MST continuum model for n‐octanol. Following our previous studies related to the MST parametrization for water, chloroform, and carbon tetrachloride, a detailed exploration of the definition of the solute/solvent interface has been performed. To this end, we have exploited the results obtained from free energy calculations coupled to Monte Carlo simulations, and those derived from the QM/MM analysis of solvent‐induced dipoles for selected solutes. The atomic hardness parameters have been determined by fitting to the experimental free energies of solvation in octanol. The final MST model is able to reproduce the experimental free energy of solvation for 62 compounds and the octanol/water partition coefficient (log Pow) for 75 compounds with a root‐mean‐square deviation of 0.6 kcal/mol and 0.4 (in units of log P), respectively. The model has been further verified by calculating the octanol/water partition coefficient for a set of 27 drugs, which were not considered in the parametrization set. A good agreement is found between predicted and experimental values of log Po/w, as noted in a root‐mean‐square deviation of 0.75 units of log P. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1180–1193, 2001
TL;DR: A new intermolecular force field for nitrogen atoms in organic molecules was derived from a training dataset of 76 observed azahydrocarbon crystal structures and 11 observed heats of sublimation, with agreement with their observed crystal structures usually less than 2%.
Abstract: A new intermolecular force field for nitrogen atoms in organic molecules was derived from a training dataset of 76 observed azahydrocarbon crystal structures and 11 observed heats of sublimation. The previously published W99 force field for hydrogen, carbon, and oxygen was thus extended to include nitrogen atoms. Nitrogen atoms were divided into four classes: N(1) for triply bonded nitrogen, N(2) for nitrogen with no bonded hydrogen (except the triple bonded case), N(3) for nitrogen with one bonded hydrogen, and N(4) for nitrogen with two or more bonded hydrogens. H(4) designated hydrogen bonded to nitrogen. Wavefunctions of 6-31g** quality were calculated for each molecule and the molecular electric potential (MEP) was modeled with net atomic and supplementary site charges. Lone pair electron charge sites were included for nitrogen atoms where appropriate, and methylene bisector charges were used for CH2 and CH3 groups when fitting the MEP. XH bond distances were set to standard values for the wave function calculation and then foreshortened by 0.1 A for the MEP and force field fitting. Using the force field optimized to the training dataset, each azahydrocarbon crystal structure was relaxed by intermolecular energy minimization. Predicted maximum changes in unit cell edge lengths for each crystal were 3% or less. The complete force field for H, C, N, and O atoms was tested by intermolecular energy relaxation of nucleoside and peptide molecular crystals. Even though these molecules were not included in any of the training datasets for the force field, agreement with their observed crystal structures was very good, with predicted unit cell edge shifts usually less than 2%. These tests included crystal structures of representatives of all eight common nucleosides found in DNA and RNA, 15 dipeptides, four tripeptides, two tetrapeptides, and a pentapeptide with two molecules in the asymmetric unit. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1154–1166, 2001
TL;DR: Parameterization and test calculations of a reduced protein model with new energy terms are presented, which retain the steric properties and the most significant degrees of freedom of protein side chains in an efficient way using only one to three virtual atoms per amino acid residue.
Abstract: Parameterization and test calculations of a reduced protein model with new energy terms are presented. The new energy terms retain the steric properties and the most significant degrees of freedom of protein side chains in an efficient way using only one to three virtual atoms per amino acid residue. The energy terms are implemented in a force field containing predefined secondary structure elements as constraints, electrostatic interaction terms, and a solvent-accessible surface area term to include the effect of solvation. In the force field the main-chain peptide units are modeled as electric dipoles, which have constant directions in α-helices and β-sheets and variable conformation-dependent directions in loops. Protein secondary structures can be readily modeled using these dipole terms. Parameters of the force field were derived using a large set of experimental protein structures and refined by minimizing RMS errors between the experimental structures and structures generated using molecular dynamics simulations. The final average RMS error was 3.7 A for the main-chain virtual atoms (Cα atoms) and 4.2 A for all virtual atoms for a test set of 10 proteins with 58–294 amino acid residues. The force field was further tested with a substantially larger test set of 608 proteins yielding somewhat lower accuracy. The fold recognition capabilities of the force field were also evaluated using a set of 27,814 misfolded decoy structures. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1229–1242, 2001
TL;DR: It seems that after appropriate parameterizations, a simple harmonic molecular model, such as employed in AMBER, can also reproduce lower vibrational frequencies of molecules quite well.
Abstract: Parmscan is an automatic engine for force-field parameterization. In this work, we applied both systematic search (SS) and a genetic algorithm (GA) to optimize the force-field parameters (bond length, bond angle, as well as torsional angle terms) to reproduce the relative energies of conformational pairs as well as other molecular properties such as vibrational frequencies. We present an example of how to apply Parmscan to reproduce the relative energies of 11 hydrocarbons by optimizing the torsional parameter of C–C–C–C using both systematic search and the genetic algorithm. Both of the two methods successfully found the lowest RMS error, which is 0.51 kcal/mol (the unsigned mean error is 0.37 kcal/mol). The Cornell et al. model (Parm94, ref. 21) achieves an RMS error of 0.78 kcal/mol. A second example is the application of the genetic algorithm to optimize the torsional parameter C–O–C–O and bond angle parameter O–C–O simultaneously for 11 dioxanes, to reproduce the experimental relative energies. After 300–400 iterations of GA optimizations, the RMS deviation is reduced to 0.56–0.57 kcal/mol, slightly better than that of Parm99 (ref. 22) and much better than that of the Cornell et al. model. In further applications, the bond length and bond angle parameters of hydrocarbons and benzene were optimized to reproduce the experimental vibrational frequencies. Encouraging results were obtained compared to the Cornell et al. force field: for the low vibrational frequencies of ethane, propane, and butane, the new model achieves an unsigned mean error of 19 cm−1, compared to 30 cm−1 of the Cornell et al. model; for 20 vibrational frequencies of benzene, the new model can also give much smaller unsigned mean error (29 vs. 53 cm−1). It seems that after appropriate parameterizations, a simple harmonic molecular model, such as employed in AMBER, can also reproduce lower vibrational frequencies of molecules quite well. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1219–1228, 2001
TL;DR: This work has studied the binding of an octapeptide ligand to the murine MHC class I protein using both explicit solvent and implicit solvent models, and finds electrostatic interactions are found to enhance the binding affinity.
Abstract: Solvent effects play a crucial role in mediating the interactions between proteins and their ligands. Implicit solvent models offer some advantages for modeling these interactions, but they have not been parameterized on such complex problems, and therefore, it is not clear how reliable they are. We have studied the binding of an octapeptide ligand to the murine MHC class I protein using both explicit solvent and implicit solvent models. The solvation free energy calculations are more than 103 faster using the Surface Generalized Born implicit solvent model compared to FEP simulations with explicit solvent. For some of the electrostatic calculations needed to estimate the binding free energy, there is near quantitative agreement between the explicit and implicit solvent model results; overall, the qualitative trends in the binding predicted by the explicit solvent FEP simulations are reproduced by the implicit solvent model. With an appropriate choice of reference system based on the binding of the discharged ligand, electrostatic interactions are found to enhance the binding affinity because the favorable Coulomb interaction energy between the ligand and protein more than compensates for the unfavorable free energy cost of partially desolvating the ligand upon binding. Some of the effects of protein flexibility and thermal motions on charging the peptide in the solvated complex are also considered. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 591–607, 2001
TL;DR: Questions concerning modeling of ligands and the accuracy of the computational model are studied and the adequacy of the model is judged in relation to the inherent accuracy achievable with the hybrid DFT method B3LYP.
Abstract: Different models to treat metal-catalyzed enzyme reactions are investigated. The test case chosen is the recently suggested full catalytic cycle of manganese catalase including eight different steps. This cycle contains OO and OH activations, as well as electron transfer steps and redox active reactions, and is therefore believed to be representative of many similar systems. Questions concerning modeling of ligands and the accuracy of the computational model are studied. Imidazole modeling of histidines are compared to ammonia modeling, and formate modeling compared to acetate modeling of glutamates. The basis set size required for the geometry optimization and for the final energy evaluation is also investigated. The adequacy of the model is judged in relation to the inherent accuracy achievable with the hybrid DFT method B3LYP. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1634–1645, 2001
TL;DR: In this article, the structures and interaction energies of guanine and uracil quartets have been determined by B3lyP hybrid density functional calculations, which are suitable for hydrogen-bonded biological systems.
Abstract: The structures and interaction energies of guanine and uracil quartets have been determined by B3LYP hybrid density functional calculations. The total interaction energy $\Delta$E$^{T}$ of the $\it{C}$$_{4h}$-symmetric guanine quartet consisting of Hoogsteen type base pairs with two hydrogen bonds between two neighbour bases is -66.07 kcal/mol at the highest level. The uracil quartet with C6-H6...O4 interactions between the individual bases has only a small interaction energy of -20.92 kcal/mol and the interaction energy of -24.63 kcal/mol for the alternative structure with N3-H3...O4 hydrogen bonds is only slightly more negative. Cooperative effects contribute between 10 and 25 \% to all interaction energies. Complexes of metal ions with G-quartets can be classified into different structure types. The one with Ca$^{2+}$ in the central cavity adopts a $\it{C}$$_{4h}$-symmetric structure with coplanar bases, whereas the energies of the planar and non-planar Na$^{+}$ complexes are almost identical. The small ions Li$^{+}$, Be$^{2+}$, Cu$^{+}$ and Zn$^{2+}$ prefer a non-planar $\it{S}$$_{4}$-symmetric structure. The lack of co-planarity prevents probably a stacking of these base quartets. The central cavity is too small for K$^{+}$ ions and therefore this ion favours in contrast to all other investigated ions a $\it{C}$$_{4}$-symmetric complex, which is 4.73 kcal/mol more stable than the $\it{C}$$_{4h}$-symmetric one. The distance 1.665 {\AA} between K$^{+}$ and the root mean squares plane of the guanine bases is approximately half of the distance between two stacked G-quartets. The total interaction energy of alkaline earth ion complexes exceeds the ones with alkali ions. Within both groups of ions the interaction energy decreases with an increasing row position in the periodic table. The B3LYP and BLYP methods lead to similar structures and energies. Both methods are suitable for hydrogen-bonded biological systems. Compared with the before mentioned methods the HCTH functional leads to longer hydrogen bonds and different relative energies for two U-quartets. Finally we calculated also structures and relative energies with the MMFF94 forcefield. Contrary to all DFT methods, MMFF94 predicts bifurcated C-H...O contacts in the uracil quartet. In the G-quartet the MMFF94 hydrogen bond distances N2-H22...N7 are shorter than the DFT distances, whereas the N1-H1...O6 distances are longer.
TL;DR: A new similarity criterion, based on a generalized expression based on the normalized integral of a weighted crosscorrelation function, is introduced that properly recognizes shifted but otherwise similar details in spectra and that the resulting similarity measure is normalized.
Abstract: A generalized expression is given for the similarity of spectra, based on the normalized integral of a weighted crosscorrelation function. It is shown that various similarity and dissimilarity criteria previously described in literature can be written as special cases of this general expression. A new similarity criterion, based on this generalized expression, is introduced. The benefits of this criterion are that it properly recognizes shifted but otherwise similar details in spectra and that the resulting similarity measure is normalized. Moreover, the criterion can easily be adapted to specific properties of spectra resulting from various analytical methods. The new criterion is applied to the classification of a series of crystal structures of cephalosporin complexes, based on comparison of their calculated powder diffraction patterns. The results are compared with those obtained using previously described criteria. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 273–289, 2001
TL;DR: It is concluded that mPW1PW is the new reliable method, which can be used in predicting molecular structures and vibrational spectra of large coordination compounds containing platinum(II).
Abstract: A comparison of eight density functional models for predicting the molecular structures, vibrational frequencies, infrared intensities, and Raman scattering activities of platinum(II) antitumor drugs, cisplatin and carboplatin, is reported. Methods examined include the pure density functional protocols (G96LYP, G96PW91, modified mPWPW and original PW91PW91), one-parameter hybrid approaches (mPW1PW and mPW1LYP), and three-parameter hybrid models (B3LYP and B3PW91), as well as the HF and MP2 levels of theory. Different effective core potentials (ECPs) and several basis sets are considered. The theoretical results are discussed and compared with the experimental data. It is remarkable that the mPW1PW protocol introduced by Adamo and Barone (J Chem Phys 1998, 108, 664), is clearly superior to all the remaining density functional methods (including B3LYP). The geometry and vibrational frequencies of cisplatin and carboplatin calculated with the mPW1PW method, and the ECP of Hay and Wadt (LanL2DZ basis set) are in better agreement with experiment than those obtained with the MP2 method. The use of more elaborated ECP and the enlargements of basis sets do not significantly improve the results. A clear-cut assignments of the platinum-ligand vibrations in cisplatin and carboplatin are presented. It is concluded that mPW1PW is the new reliable method, which can be used in predicting molecular structures and vibrational spectra of large coordination compounds containing platinum(II). c 2001 John Wiley & Sons, Inc. J Comput Chem 22: 901-912, 2001
TL;DR: An automated computer docking program, EUDOC, is reported herein for prediction of ligand–receptor complexes from 3D receptor structures, including metalloproteins, and for identification of a subset enriched in drug leads from chemical databases.
Abstract: The completion of the Human Genome Project, the growing effort on proteomics, and the Structural Genomics Initiative have recently intensified the attention being paid to reliable computer docking programs able to identify molecules that can affect the function of a macromolecule through molecular complexation. We report herein an automated computer docking program, EUDOC, for prediction of ligand-receptor complexes from 3D receptor structures, including metalloproteins, and for identification of a subset enriched in drug leads from chemical databases. This program was evaluated from the standpoints of force field and sampling issues using 154 experimentally determined ligand-receptor complexes and four "real-life" applications of the EUDOC program. The results provide evidence for the reliability and accuracy of the EUDOC program. In addition, key principles underlying molecular recognition, and the effects of structural water molecules in the active site and different atomic charge models on docking results are discussed. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1750-1771, 2001
TL;DR: It is found that the introduction of the ligand volume correction consistently improves the correlation between the PMF scores and the measured binding affinities.
Abstract: Recently, a knowledge-based scoring function has been introduced that estimates the protein-binding affinity based on the 3D structure of a protein–ligand complex (J Med Chem 1999, 42, 791). A ligand volume correction factor has been proposed and applied to filter out intraligand interactions in this simplified potential approach. Here we evaluate the effect of the ligand volume correction on the predictive power of the PMF scoring function. It is found that the effect of the ligand volume correction is significant on the derived potentials and large on the overall score. However, the effect of the ligand correction on the predictive power of the scoring function appears to be smaller. For a test set containing serine proteases the predictive power of the PMF scoring function does not change with the introduction of the volume correction. For a test set of metalloprotease complexes, the predictive power of the PMF scoring function improves only slightly when the volume correction is applied. For five test sets comprising a total of 225 diverse protein ligand complexes taken from the Brookhaven Protein Data Bank it is found, however, that the introduction of the ligand volume correction consistently improves the correlation between the PMF scores and the measured binding affinities. The effect of the correction factor on docking/scoring experiments is also analyzed using a test set of 61 biphenyl inhibitor-stromelysin complexes. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 418–425, 2001
TL;DR: The application of the MSINDO version of the semiempirical SCF MO method SINDO1 to small transition metal complexes that were not included in the parameterization shows that the optimized parameters are transferable to other compounds.
Abstract: The recently developed MSINDO version of the semiempirical SCF MO method SINDO1 has been parameterized for third-row transition metals Sc to Zn. The set of reference data used for the previous parameterization of SINDO1 has been substantially increased by incorporating results of recent experiments and first-principles calculations. A comparison of calculated heats of formation, geometries, ionization potentials, and dipole moments with literature values for more than 200 gas phase molecules is presented. The accuracy of the modified MSINDO version achieved for heats of formation and bond lengths has been considerably improved compared to SINDO1. Small clusters of transition metals and metal oxides were included in the parameterization to ensure accurate results for studies of larger systems. The application of the method to small transition metal complexes that were not included in the parameterization shows that the optimized parameters are transferable to other compounds. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 861–887, 2001
TL;DR: A comparative study of geometrical parameters is performed on the complexes HF–HF, H2O–H2O, and HF–H3 using 12 different basis sets at the RHF, MP2, and DFT levels of theory.
Abstract: A comparative study of geometrical parameters is performed on the complexes HF-HF, H2O-H2O, and HF-H2O using 12 different basis sets at the RHF, MP2, and DFT (BLYP and B3LYP) levels of theory. The equilibrium geometries were obtained from uncorrected, a posteriori (counterpoise, CP) and ap riori(Chemical Hamiltonian Approach, CHA) BSSE-corrected potential energy surfaces. The calculation of equilibrium geometries using the CP and CHA schemes is described in details. The effect of the BSSE on various intermolecular parameters is discussed and the performance of the applied theoretical models is critically evaluated from the BSSE point of view. c 2001 John Wiley & Sons, Inc. J Comput Chem 22: 765-786, 2001
TL;DR: The accuracy with which the QMFF reproduces the ab initio molecular bond lengths, bond angles, torsional angles, vibrational frequencies, and conformational energies is given for each functional group demonstrates that the methodology is broadly applicable for the derivation of force field parameters across widely differing types of molecules.
Abstract: A class II valence force field covering a broad range of organic molecules has been derived employing ab initio quantum mechanical "observables." The procedure includes selecting representative molecules and molecular structures, and systematically sampling their energy surfaces as described by energies and energy first and second derivatives with respect to molecular deformations. In this article the procedure for fitting the force field parameters to these energies and energy derivatives is briefly reviewed. The application of the methodology to the derivation of a class II quantum mechanical force field (QMFF) for 32 organic functional groups is then described. A training set of 400 molecules spanning the 32 functional groups was used to parameterize the force field. The molecular families comprising the functional groups and, within each family, the torsional angles used to sample different conformers, are described. The number of stationary points (equilibria and transition states) for these molecules is given for each functional group. This set contains 1324 stationary structures, with 718 minimum energy structures and 606 transition states. The quality of the fit to the quantum data is gauged based on the deviations between the ab initio and force field energies and energy derivatives. The accuracy with which the QMFF reproduces the ab initio molecular bond lengths, bond angles, torsional angles, vibrational frequencies, and conformational energies is then given for each functional group. Consistently good accuracy is found for these computed properties for the various types of molecules. This demonstrates that the methodology is broadly applicable for the derivation of force field parameters across widely differing types of molecular structures. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1782-1800, 2001
TL;DR: D density functional calculations are carried out for the Sc3−nLanN@C80 (n=0–3) series to provide theoretical insight into the structures and properties of Sc3N@ C80, which has been isolated in high yield and purity as a new stable endohedral metallofullerene.
Abstract: To provide theoretical insight into the structures and properties of Sc3N@C80, which has been isolated in high yield and purity as a new stable endohedral metallofullerene, density functional calculations are carried out for the Sc3−nLanN@C80 (n=0–3) series. Because of electron transfer from Sc3N to C80, the electronic structure of Sc3N@C80 is formally described as (Sc3N)6+C\\documentclass{article}\\pagestyle{empty}\\begin{document}$_{80}^{6-}$\\end{document}. The encapsulated Sc3N cluster takes a planar structure with long Sc–Sc distances and is highly stabilized inside the Ih cage of C80, which rotates rapidly. As the number of La atoms increases, the Sc3−nLanN cluster is forced to maintain a pyramidal structure in Sc3−nLanN@C80. In addition, the C80 cage takes an open‐shell electronic structure due to an increase in the number of electrons transferring from Sc3−nLanN. These make the endohedral structure less stable and more reactive. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1353–1358, 2001
TL;DR: In this paper, the authors used the HF/6-31G ∗ level of theory to calculate relaxed potential energy surfaces for 12 analogs of disaccharides, which were made by replacing glucose with tetrahydropyran and fructose with 2-methyltetrahydrofuran.
Abstract: The HF/6-31G ∗ level of theory was used to calculate relaxed potential energy surfaces for 12 analogs of disaccharides. The analogs were made by replacing glucose with tetrahydropyran and fructose with 2-methyltetrahydrofuran. Molecules had zero, one or two anomeric carbon atoms, and di-axial, axial-equatorial, and di-equatorial linkages. Despite the absence of hydroxyl groups, the surfaces account well for conformations that are observed in crystals of the parent disaccharides. Thus, torsional energy and the simple bulk of ring structures are major factors in determining disaccharide conformation. The contour shapes around the global minima depend on the number of anomeric carbons involved in the linkage, while the presence of alternative minima that have relative energies less than 4 kcal/mol mostly requires equatorial bonds. However, molecules with two adjacent anomeric centers gave exceptions to these rules. Flexibility values related to a partition function show that the di-axial trehalose analog is the most rigid. The di-equatorial pseudodisaccharide analog with no anomeric centers is most flexible. Reproduction of these surfaces is proposed as a simple test of force fields for modeling carbohydrates. Also, these surfaces can be used in a simple hybrid method for calculating disaccharide energy surfaces. c 2000 John Wiley &
TL;DR: Accurate reproduction of the increase in solution density with addition of salt was found while the electrical conductivity of PEO/LiPF6 solutions was found to be within an order of magnitude of the experimental values.
Abstract: Ab initio and molecular mechanics studies of LiPF6 and the interaction of the salt with the poly(ethylene oxide) (PEO) oligomer dimethylether have been performed. Optimized geometries and energies of Li+/PF6− complexes obtained from quantum chemistry revealed a preference for C3V symmetry structures for Li+–P separations under 2.8 A, C2V symmetry for Li+–P in the range of 2.8–3.3 A and C4V symmetry for Li+–P separations larger than 3.3 A. Electron correlation effects were found to make an insignificant contribution to binding in the Li+/PF6− complex. By contrast, analogous studies of PF6−/PF6− and PF6−/dimethyl ether complexes revealed important contributions of electron correlation to the complex interaction energy. A molecular mechanics force field for simulations of PEO/LiPF6 melts was parameterized to reproduce the geometries and energies of Li+/PF6−, PF6−/PF6−, PF6−/dimethylether complexes. Molecular dynamics simulations of PEO/LiPF6 melts were performed to validate this quantum chemistry-based force field. Accurate reproduction of the increase in solution density with addition of salt was found while the electrical conductivity of PEO/LiPF6 solutions was found to be within an order of magnitude of the experimental values. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 641–654, 2001
TL;DR: Two approaches for determining atomic volumes for the generalized Born model are described; one is based on Voronoi polyhedra and the other, on minimizing the fluctuations in the overall volume of the solute.
Abstract: An essential element of implicit solvent models, such as the generalized Born method, is a knowledge of the volume associated with the individual atoms of the solute. Two approaches for determining atomic volumes for the generalized Born model are described; one is based on Voronoi polyhedra and the other, on minimizing the fluctuations in the overall volume of the solute. Volumes to be used with various parameter sets for protein and nucleic acids in the CHARMM force field are determined from a large set of known structures. The volumes resulting from the two different approaches are compared with respect to various parameters, including the size and solvent accessibility of the structures from which they are determined. The question of whether to include hydrogens in the atomic representation of the solute volume is examined. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1857-1879, 2001
TL;DR: Application of this method to selected proteins shows that it can detect the best fold family that is closest to native, along with several other misfolded families, and a method to obtain substructures is described.
Abstract: Current ab initio structure-prediction methods are sometimes able to generate families of folds, one of which is native, but are unable to single out the native one due to imperfections in the folding potentials and an inability to conduct thorough explorations of the conformational space. To address this issue, here we describe a method for the detection of statistically significant folds from a pool of predicted structures. Our approach consists of clustering and averaging the structures into representative fold families. Using a metric derived from the root-mean-square distance (RMSD) that is less sensitive to protein size, we determine whether the simulated structures are clustered in relation to a group of random structures. The clustering method searches for cluster centers and iteratively calculates the clusters and their respective centroids. The centroid interresidue distances are adjusted by minimizing a potential constructed from the corresponding average distances of the cluster structures. Application of this method to selected proteins shows that it can detect the best fold family that is closest to native, along with several other misfolded families. We also describe a method to obtain substructures. This is useful when the folding simulation fails to give a total topology prediction but produces common subelements among the structures. We have created a web server that clusters user submitted structures, which can be found at http://bioinformatics.danforthcenter.org/services/scar. c 2001 John Wiley & Sons, Inc. J Comput Chem 22: 339-353, 2001