Cumulative atomic multipole representation of the molecular charge distribution and its basis set dependence

A simple procedure to decompose the theoretical molecular charge distribution into cumulative atomic multipoles supplementing any population analysis scheme has been described and tested for a number of molecules in extended basis sets. This approach may be applied to describe local charge distributions in neutral as well as charged systems and also leads to a simplified point-charge model conserving the local anisotropy of the atomic charge distribution in molecules. Such an approach may be useful in estimating intermolecular interactions, representing the molecular environment in solvent effect or enzyme catalytic activity studies, evaluation of molecular electrostatic potentials or tracing the quality of basis set functions.     

Structural character and energetics of tyrosyl radical formation by electron/proton transfers of a covalently linked histidine-tyrosine: a model for cytochrome C oxidase

The structural, energetic, and electronic and IR spectroscopic properties for a model of the cross-linked histidine-tyrosine (His-Tyr) residues as found in cytochrome c oxidase (CcO) are investigated by ab initio methods. The formation of a His-Tyr radical is studied by two paths: proton release followed by electron release and vice versa. The energetics for the proton/electron releases of the Tyr depend modestly on the cross-linked His substituent and, more sensitively, on the charge of the cation attached to the imino N site of the His residue. Protonation of the imino N site significantly increases the electron ionization potential and decreases the proton dissociation energy, making them competitive processes. A positive charge placed at the imino N site, whose value is scanned from zero to one, shows a continuous increase in ionization potential and a decrease in proton dissociation energy, with the +1 limit agreeing well with the protonated imino N site result, indicating a dominant electrostatic effect. The charge populations and the spin density distributions of the His-Tyr model, the radical cation formed by electron ionization, the anion formed by proton dissociation, and the final His-Tyr radical depend sensitively on the substituents, implying a modulation role on the charge transfer between the phenol and imidazole rings, especially for the charged species. His-Tyr and protonated His-Tyr exhibit differences among their respective structural isomers with consequences on their IR absorptions. Small barriers between their pseudo-cis and pseudo-trans rotamers demonstrate the relative flexibility between the two rings, and these may facilitate proton release and charge transfer. The cation effect demonstrates that the cationized cross-linked His-Tyr should be the best candidate to mimic the covalently ring-linked histidine-tyrosine structure in CcO.     

甲硫氨酸-脑啡肽的活性位点

用ＡＭ１方法中计算静电势的ＰＭＥＰ子程序了甲硫氨酸－脑啡肽的活性位点。通过计算得到了整个分子的三维空间静电势分布和由静电势导出的各原子的电荷分布。进一步分析,确定模型分子活性位点为酪氨酸残在的叔氨原子和苯酚基、苯丙氨酸残基的苯基及部分氧原子。     

Topological features of both electron density and electrostatic potential in the bis(thiosemicarbazide)zinc(II) dinitrate complex

The experimental electron density of the bis(thiosemicarbazide)zinc(II) dinitrate complex, [Zn(CH5N3S)2](NO3)2,was studied. The Hansen-Coppens multipole model was used to extract the electron density from high-resolution X-ray diffraction data collected at 100 K. Careful strategies were designed for the electron density refinements regarding the charge transfer between the anionic and the cationic parts of the complex. Particular attention was also paid to the treatment of the electron density of the zinc atom interacting with two thiosemicarbazide ligands in a tetrahedral coordination. Nevertheless, the filled 3d valence shell of Zn was found unperturbed, and only the 4s shell was engaged in the metal-ligand interaction. Topological properties of both electron density and electrostatic potential, including kinetic and potential energy densities, and atomic charges were reported to quantify a metal-ligand complex with particular Zn-S and Zn-N bonds and hydrogen-bonding features. Chemical activities were screened through the molecular surface on which the three-dimensional electrostatic potential function was projected. The experimental results were compared to those obtained from gas-phase quantum calculations, and a good agreement was reached between these two approaches. Finally, among other electrostatic potential critical points, the values at the maxima corresponding to the nuclear sites were used as indices of the hydrogen-bonding capacity of the thiosemicarbazide ligand.     

Accurate modeling of the intramolecular electrostatic energy of proteins

The (?, ψ) energy surface of blocked alanine (N-acetyl–N′-methyl alanineamide) was calculated at the Hartree-Fock (HF)/6-31G* level using ab initio molecular orbital theory. A collection of six electrostatic models was constructed, and the term electrostatic model was used to refer to (1) a set of atomic charge densities, each unable to deform with conformation; and (2) a rule for estimating the electrostatic interaction energy between a pair of atomic charge densities. In addition to two partial charge and three multipole electrostatic models, this collection includes one extremely detailed model, which we refer to as nonspherical CPK. For each of these six electrostatic models, parameters—in the form of partial charges, atomic multipoles, or generalized atomic densities—were calculated from the HF/6-31G* wave functions whose energies define the ab initio energy surface. This calculation of parameters was complicated by a problem that was found to originate from the locking in of a set of atomic charge densities, each of which contains a small polarization-induced deformation from its idealized unpolarized state. It was observed that the collective contribution of these small polarization-induced deformations to electrostatic energy differences between conformations can become large relative to ab initio energy differences between conformations. For each of the six electrostatic models, this contribution was reduced by an averaging of atomic charge densities (or electrostatic energy surfaces) over a large collection of conformations. The ab initio energy surface was used as a target with respect to which relative accuracies were determined for the six electrostatic models. A collection of 42 more complete molecular mechanics models was created by combining each of our six electrostatic models with a collection of seven models of repulsion + dispersion + intrinsic torsional energy, chosen to provide a representative sample of functional forms and parameter sets. A measure of distance was defined between model and ab initio energy surfaces; and distances were calculated for each of our 42 molecular mechanics models. For most of our 12 standard molecular mechanics models, the average error between model and ab initio energy surfaces is greater than 1.5 kcal/mol. This error is decreased by (1) careful treatment of the nonspherical nature of atomic charge densities, and (2) accurate representation of electrostatic interaction energies of types 1—2 and 1—3. This result suggests an electrostatic origin for at least part of the error between standard model and ab initio energy surfaces. Given the range of functional forms that is used by the current generation of protein potential functions, these errors cannot be corrected by compensating for errors in other energy components. © 1995 by John Wiley & Sons, Inc.     

A molecular electrostatic-potential study of acesulfame

Molecular electrostatic-potential maps are reported for the anionic and neutral forms of acesulfame (6-methyl-1,2,3-oxathiazin-4(3H)-one-2,2-dioxide), a sweetener structurally similar to saccharin. The maps generated by methods based on a minimum basis set (STO-3G) and on a polarization basis set (3-21G*) are almost identical with respect to their contour levels. From the contour maps, broad and deep electrostatic-potential minima were found near the SO₂ and NC=O functionalities in the anion. The electrostatic potential minima directly correspond to the reactive sites proposed by Jakinovich for the interaction fo saccharin with its receptor.     

Interference between the hydrogen bonds to the two rings of nicotine

The biochemical transport and binding of nicotine depends on the hydrogen bonding between water and binding site residues to the pyridine ring and the protonated pyrrolidinium ring. To test the independence of these two moderately separated hydrogen-bonding sites, we have calculated the structures of clusters of protonated nicotine with water and a bicarbonate anion, benzene, indole, or a second water molecule. Unprotonated nicotine-water clusters have also been studied for contrast. The potential energy surfaces are first explored with an intermolecular anisotropic atom-atom model potential. Full geometry optimizations are then carried out using density functional theory to include nonadditive terms in the interaction energies. The presence of the charge on the pyrrolidine nitrogen removes the conventional hydrogen-bonding site on the pyridine ring. The hydrogen-bond ability of this site is nearly recovered when the protonated pyrrolidinium ring is bound to a bicarbonate anion, whereas its interaction with benzene shows a much smaller effect. Indole appears to partially restore the hydrogen-bond ability of the pyridine nitrogen, although indole and benzene both pi-bond to the pyrrolidinium ring. A second hydrogen-bonding water produces a significant conformational distortion of the nicotine. This demonstrates the limitations of the conventional qualitative predictions of hydrogen bonding based on the independence of molecular fragments. It also provides benchmarks for the development of atomistic modeling of biochemical systems.     

Multipole correction of atomic monopole models of molecular charge distribution. I. Peptides

The defects in atomic monopole models of molecular charge distribution have been analyzed for several model-blocked peptides and compared with accurate quantum chemical values. The results indicate that the angular characteristics of the molecular electrostatic potential around functional groups capable of forming hydrogen bonds can be considerably distorted within various models relying upon isotropic atomic charges only. It is shown that these defects can be corrected by augmenting the atomic point charge models by cumulative atomic multipole moments (CAMMs). Alternatively, sets of off-center atomic point charges could be automatically derived from respective multipoles, providing approximately equivalent corrections. For the first time, correlated atomic multipoles have been calculated for N-acetyl, N'-methylamide-blocked derivatives of glycine, alanine, cysteine, threonine, leucine, lysine, and serine using the MP2 method. The role of the correlation effects in the peptide molecular charge distribution are discussed.     

On the use of AM1 and MNDO wave functions to compute accurate electrostatic charges

A new strategy to evaluate accurate electrostatic charges from semiempirical wave functions is reported. The rigorous quantum mechanical molecular electrostatic potentials computed from both MNDO and AM1 wave functions are fitted to the point-charge molecular electrostatic potential to obtain the electrostatic charges. The reliability of this strategy is tested by comparing the semiempirical electrostatic charges for 21 molecules with the semiempirical Mulliken charges and with the ab initio STO-3G and 6-31G* electrostatic charges. The ability of the dipoles derived from the semiempirical electrostatic and Mulliken charges as well as from the SCF charge distributions to reproduce the ab initio 6-31G* electrostatic dipoles and the gas phase experimental values is determined. The statistical analysis clearly point out the goodness of the semiempirical electrostatic charges, specially when the MNDO method is used. The excellent relationships found between the MNDO and 6-31G* electrostatic charges permit to define a scaling factor which allows to accurately reproduce the 6-31G* electrostatic charge distribution as well as the experimental dipoles from the semiempirical electrostatic charges.     

Experimental charge density study of estrogens: 17beta-estradiol.urea

To relate the molecular electrostatic potential to the biological activities of estrogens, a comparative charge density study of different derivatives has been initiated. The second completed charge density analysis of this series for 17beta-estradiol*urea is presented here. This is a large organic system with 52 atoms in a noncentrosymmetric space group, therefore special tools such as an optimal coordinate system and slow, initially constrained refinement have been used to accomplish this study. Our results for the urea molecule reasonably agree with previous experimental and theoretical results. In the 17beta-estradiol molecule, the oxygen atoms appear to be close to sp3 in shape, exhibiting two consistent, distinct lone pairs despite different chemical environments. No significant interaction of the hydroxyl group oxygen with the orbitals of the aromatic ring is observed. Analysis of the electrostatic potential revealed that the negative potential in the lone pair region of the two oxygen atoms is quite different. The topological analysis of the electron density has been performed, and the atomic charges have been estimated.     

Effect of hydration on the FH... NH3 proton transfer reaction: Comparison of some quantum chemical approximations

The proton transfer energy curve for the hydrogen fluoride-ammonia system was studied by semi-empirical methodsin vacuo and in a hydrated form. It was found that the simple point-charge approximation cannot be used to estimate the Coulombic interaction term rather the molecular electrostatic potential has to be considered. Furthermore, even inclusion of the mutual polarization term is insufficient if quantitative agreement with CNDO/2 supermolecule results is desired since charge transfer plays an important role.     

Dynamic and electrostatic effects in enzymatic processes. An analysis of the nucleophilic substitution reaction in haloalkane dehalogenase

We present an analysis of rare event trajectories for the nucleophilic displacement of a chloride anion of 1,2-dichloroethane by a carboxylate group in haloalkane dehalogenase from Xanthobacterautotrophicus (DhlA) and in aqueous solution. Differences in the transmission coefficient are rationalized on the basis of the electrostatic coupling between the chemical system and the environment. Detailed analysis of the reactive trajectories reveals that the evolution of the hydrogen bond interactions established between the substrate and the environment present significant differences in aqueous solution and in the enzyme. The structure of the enzymatic active site provides a more adequate interaction pattern for the reaction progress.     

Ab initio molecular dynamics of heme in cytochrome c

Ab initio molecular dynamics (AIMD) calculations, based on the Car-Parrinello method, have been carried out for three models of heme c that is present in cytochrome c. Both the reduced (Fe(II)) and oxidized (Fe(III)) forms have been analyzed. The simplest models (1R and 1O, respectively) consist of a unsubstituted porphyrin (with no side chains) and two axially coordinated imidazole and ethylmethylthioether ligands. Density functional theory optimizations of these models confirm the basic electronic features and are the starting point for building more complex derivatives. AIMD simulations were performed after reaching the thermal stability at T = 300 K. The evolution of the Fe-L(ax) bond strengths is examined together with the relative rotations of the imidazole and methionine about the axial vector, which appear rather independent from each other. The next models (2R and 2O) contain side chains at the heme to better simulate the actual active site. It is observed that two adjacent propionate groups induce some important effects. The axial Fe-Sdelta bond is only weakened in 2R but is definitely cleaved in the oxidized species 2O. Also the mobility of the Im ligand seems to be reduced by the formation of a strong hydrogen bond that involves the Im Ndelta1-Hdelta1 bond and one carboxylate group. In 2O the interaction becomes so strong that a proton transfer occurs and the propionic acid is formed. Finally, the models 3 include a free N-methyl-acetamide molecule to mimic a portion of the protein backbone. This influences the orientation of carboxylate groups and limits the amount of their hydrogen bonding with the Im ligand. Residual electrostatic interactions are maintained, which are still able to modulate the dissociation of the methionine from the heme.     

Force-field development and molecular dynamics simulations of ferrocene-peptide conjugates as a scaffold for hydrogenase mimics

The increasing importance of hydrogenase enzymes in the new energy research field has led us to examine the structure and dynamics of potential hydrogenase mimics, based on a ferrocene-peptide scaffold, using molecular dynamics (MD) simulations. To enable this MD study, a molecular mechanics force field for ferrocene-bearing peptides was developed and implemented in the CHARMM simulation package, thus extending the usefulness of the package into peptide-bioorganometallic chemistry. Using the automated frequency-matching method (AFMM), optimized intramolecular force-field parameters were generated through quantum chemical reference normal modes. The partial charges for ferrocene were derived by fitting point charges to quantum-chemically computed electrostatic potentials. The force field was tested against experimental X-ray crystal structures of dipeptide derivatives of ferrocene-1,1'-dicarboxylic acid. The calculations reproduce accurately the molecular geometries, including the characteristic C2-symmetrical intramolecular hydrogen-bonding pattern, that were stable over 0.1 micros MD simulations. The crystal packing properties of ferrocene-1-(D)alanine-(D)proline-1'-(D)alanine-(D)proline were also accurately reproduced. The lattice parameters of this crystal were conserved during a 0.1 micros MD simulation and match the experimental values almost exactly. Simulations of the peptides in dichloromethane are also in good agreement with experimental NMR and circular dichroism (CD) data in solution. The developed force field was used to perform MD simulations on novel, as yet unsynthesized peptide fragments that surround the active site of [Ni-Fe] hydrogenase. The results of this simulation lead us to propose an improved design for synthetic peptide-based hydrogenase models. The presented MD simulation results of metallocenes thereby provide a convincing validation of our proposal to use ferrocene-peptides as minimal enzyme mimics.     

THE 'OPSIN SHIFT' IN BACTERIORHODOPSIN: STUDIES WITH ARTIFICIAL BACTERIORHODOPSINS

Abstract— The difference (in cm⁻¹) in absorption maxima between the protonated Schiff base of retinals and the pigment derived therefrom has been defined as the opsin shift. It represents the influence of the opsin binding site on the chromophore. The analysis of the opsin shifts of a series of dihydrobacteriorhodopsins has led to the external point-charge model, which in addition to a counter anion near the Schiff base ammonium, carries another negative charge in the vicinity of the β-ionone ring. This is in striking contrast to the external point-charge model proposed earlier for the bovine visual pigment. The absorption maxima of rhodopsins formed from bromo- and phenyl retinals support the two models. A retinal carrying a photoaffinity label has yielded a nonbleachable bacteriorhodopsin.     

Structure and interaction between the [BMIM][Ala] alanine anion and the 1-butyl-3-methylimidazolium cation in ion pairs

The equilibrium geometries and vibrational frequencies of the ionic liquid 1-butyl-3-methylimidazolium cation and the alanine anion [BMIM][Ala] are studied using density functional theory (DFT) at the B3PW91/6-311+G(d,p) leve1. The most stable structures of the anion, the cation, and the ion pairs are obtained and characterized, and the geometry parameters of the ion pairs confirm the presence of a hydrogen bonding interaction between the anion and the cation. Natural bond orbital (NBO) analysis is also performed to analyze the atomic charge distribution and charge transfer in the [BMIM]⁺ cation and [BMIM][Ala] ionic liquids. The results show that there are the electrostatic interaction and multiple hydrogen bond interactions between the cation and the anion of the ionic liquids, and the stability of the ground state of the ion pairs mostly results from the hydrogen bonding between the lone pairs of O atoms in the anion and H in the imidazole cycle of the cation. There are some changes in microstructures and the charge distribution during the formation of the ion pairs.     

Simulation of liquid imidazole using a high-rank quantum topological electrostatic potential

Rigid body molecular dynamics simulations were carried out on pure liquid imidazole at four different temperatures and at 1 atm. Imidazole, which is important both in life science and materials science, is one of the simplest molecules to possess both a lone pair and a π system. These two features are known to benefit from multipolar electrostatics. Here the electrostatic interaction is governed by atomic multipole moments obtained from topologically partitioned ab initio electron densities. The non-electrostatic terms are modeled with Lennard-Jones parameters adjusted to fit the experimental liquid density. All σ values are incrementally increased by one single scaling factor. We report on how the presence of multipolar electrostatics influences the local structure, dynamics and thermodynamics of the liquid compared to electrostatics by atomic point charges. The point charge force field exaggerates the number of π-stacked dimers in the liquid, and underestimates the number of hydrogen-bonded dimers. The effect of the temperature on the local structure of liquid imidazole was analysed using radial and spatial distribution functions.