QM/MM connection atoms for the multistate treatment of organic and biological molecules

We present an extension of our semiempirical floating occupation MO-CI approach for the determination of ground and excited state potential energy surfaces of interest in photochemistry. The QM/MM variant of the method, which allows for electrostatic and van der Waals interactions between the QM and MM subsystems, is supplemented with a treatment of covalent interactions based on Antes and Thiels connection atom approach. We concentrate on the correct treatment of electrostatic interactions concerning the connection atom, on the specific requirements for the representation of excited states, and on the transferability of the optimal parameters. We show the viability of the method with four examples of connection atoms: S in a thioether bridge, acylic C, aliphatic C, and N in a peptide. The results obtained with the QM/MM treatment compare well with all-QM results of the same level.     

Importance of van der Waals Interactions in QM/MM Simulations

The importance of accurately treating van der Waals interactions between the quantum mechanical (QM) and molecular mechanical (MM) atoms in hybrid QM/MM simulations has been investigated systematically. First, a set of van der Waals (vdW) parameters was optimized for an approximate density functional method, the self-consistent charge-tight binding density functional (SCC-DFTB) approach, based on small hydrogen-bonding clusters. The sensitivity of condensed phase observables to the SCC-DFTB vdW parameters was then quantitatively investigated by SCC-DFTB/MM simulations of several model systems using the optimized set and two sets of extreme vdW parameters selected from the CHARMM22 forcefield. The model systems include a model FAD molecule in solution and a solvated enediolate, and the properties studied include the radial distribution functions of water molecules around the solute (model FAD and enediolate), the reduction potential of the model FAD and the potential of mean force for an intramolecular proton transfer in the enediolate. Although there are noticeable differences between parameter sets for gas-phase clusters and solvent structures around the solute, thermodynamic quantities in the condensed phase (e.g., reduction potential and potential of mean force) were found to be less sensitive to the numerical values of vdW parameters. The differences between SCC-DFTB/MM results with the three vdW parameter sets for SCC-DFTB atoms were explained in terms of the effects of the parameter set on solvation. The current study has made it clear that efforts in improving the reliability of QM/MM methods for energetical properties in the condensed phase should focus on components other than van der Waals interactions between QM and MM atoms.     

A systematic approach to calibrate a transferable polarizable force field parameter set for primary alcohols

In this work, parameters are optimized for a charge‐on‐spring based polarizable force field for linear alcohols. We show that parameter transferability can be obtained using a systematic approach in which the effects of parameter changes on physico‐chemical properties calculated from simulation are predicted. Our previously described QM/MM calculations are used to attribute condensed‐phase polarizabilities, and starting from the non‐polarizable GROMOS 53A5/53A6 parameter set, van der Waals and Coulomb interaction parameters are optimized to reproduce pure‐liquid (thermodynamic, dielectric, and transport) properties, as well as hydration free energies. For a large set of models, which were obtained by combining small perturbations of 10 distinct parameters, values for pure‐liquid properties of the series methanol to butanol were close to experiment. From this large set of models, we selected 34 models without special repulsive van der Waals parameters to distinguish between hydrogen‐bonding and non‐hydrogen‐bonding atom pairs, to make the force field simple and transparent. © 2017 Wiley Periodicals, Inc.     

Van der Waals surface graphs and molecular shape

A van der Waals surface graph is the graph defined on a van der Waals surface by the intersections of the atomic van der Waals spheres. A van der Waals shape graph has a vertex for each atom with a visible face on the van der Waals surface, and edges between vertices representing atoms with adjacent faces on the van der Waals surface. These are discrete invariants of three‐dimensional molecular shape. Some basic properties of van der Waals surface graphs are studied, including their relationship with the Voronoi diagram of the atom centres, and a class of molecular embeddings is identified for which the dual of the van der Waals surface graph coincides with the van der Waals shape graph. This revised version was published online in July 2006 with corrections to the Cover Date.     

Van der Waals interactions: evaluations by use of a statistical mechanical method

In this work the induced van der Waals interaction between a pair of neutral atoms or molecules is considered by use of a statistical mechanical method. With use of the Schro?dinger equation this interaction can be obtained by standard quantum mechanical perturbation theory to second order. However, the latter is restricted to electrostatic interactions between dipole moments. So with radiating dipole-dipole interaction where retardation effects are important for large separations of the particles, other methods are needed, and the resulting induced interaction is the Casimir-Polder interaction usually obtained by field theory. It can also be evaluated, however, by a statistical mechanical method that utilizes the path integral representation. We here show explicitly by use of this method the equivalence of the Casimir-Polder interaction and the van der Waals interaction based upon the Schro?dinger equation. The equivalence is to leading order for short separations where retardation effects can be neglected. In recent works [J. S. H?ye, Physica A 389, 1380 (2010); Phys. Rev. E 81, 061114 (2010)], the Casimir-Polder or Casimir energy was added as a correction to calculations of systems like the electron clouds of molecules. The equivalence to van der Waals interactions indicates that the added Casimir energy will improve the accuracy of calculated molecular energies. Thus, we give numerical estimates of this energy including analysis and estimates for the uniform electron gas.     

Time-dependent density functional theory calculation of van der Waals coefficient of sodium clusters

In this paper we employ all-electron ab initio time-dependent density functional theory based method to calculate the long range dipole-dipole dispersion coefficient (van der Waals coefficient) C(6) of sodium atom clusters containing even number of atoms ranging from 2 to 20 atoms. The dispersion coefficients are obtained via Casimir-Polder relation [Phys. Rev. 3, 360 (1948)]. The calculations are carried out with two different exchange-correlation potentials: (i) the asymptotically correct statistical average of orbital potential (SAOP) and (ii) Vosko-Wilk-Nusair representation [Can. J. Phys. 58, 1200 (1980)] of exchange-correlation potential within local density approximation. A comparison with the other theoretical results has been performed. We also present the results for the static polarizabilities of sodium clusters and also compare them with other theoretical and experimental results. These comparisons reveal that the SAOP results for C(6) and static polarizability are quite accurate and very close to the experimental results. We examine the relationship between volume of the cluster and van der Waals coefficient, and find that to a very high degree of correlation C(6) scales as the square of the volume. We also present the results for van der Waals coefficient corresponding to cluster-Ar atom and cluster-N(2) molecule interactions.     

A critical evaluation of different QM/MM frontier treatments with SCC-DFTB as the QM method

The performance of different link atom based frontier treatments in QM/MM simulations was evaluated critically with SCC-DFTB as the QM method. In addition to the analysis of gas-phase molecules as in previous studies, an important element of the present work is that chemical reactions in realistic enzyme systems were also examined. The schemes tested include all options available in the program CHARMM for SCC-DFTB/MM simulation, which treat electrostatic interactions due to the MM atoms close to the QM/MM boundary in different ways. In addition, a new approach, the divided frontier charge (DIV), has been implemented in which the partial charge associated with the frontier MM atom ("link host") is evenly distributed to the other MM atoms in the same group. The performance of these schemes was evaluated based on properties including proton affinities, deprotonation energies, dipole moments, and energetics of proton transfer reactions. Similar to previous work, it was found that calculated proton affinities and deprotonation energies of alcohols, carbonic acids, amino acids, and model DNA bases are very sensitive to the link atom scheme; the commonly used single link atom approach often gives error on the order of 15 to 20 kcal/mol. Other schemes give better and, on average, mutually comparable results. For proton transfer reactions, encouragingly, both activation barriers and reaction energies are fairly insensitive (within a typical range of 2-4 kcal/mol) to the link atom scheme due to error cancellation, and this was observed for both gas-phase and enzyme systems. Therefore, the effect of using different link atom schemes in QM/MM simulations is rather small for chemical reactions that conserve the total charge. Although the current study used an approximate DFT method as the QM level, the observed trends are expected to be applicable to QM/MM methods with use of other QM approaches. This observation does not mean to encourage QM/MM simulations without careful benchmark in the study of specific systems, rather it emphasizes that other technical details, such as the treatment of long-range electrostatics, tend to play a more important role and need to be handled carefully.     

Fully retarded van der Waals interaction between dielectric nanoclusters

The van der Waals (dispersion) interaction between an atom and a cluster or between two clusters at large separation is calculated by considering each cluster as a point particle, characterized by a polarizability tensor. For the extreme limit of very large separation, the fully retarded regime, one needs to know just the static polarizability in order to determine the interaction. This polarizability is evaluated by including all many-body (MB) intracluster atomic interactions self-consistently. The results of these calculations are compared with those obtained from various alternative methods. One is to consider each cluster as a collection of many atoms and evaluate the sum of two-body interatomic interactions, a common assumption. An alternative method is to include three-body atomic interactions as a MB correction term in the total energy. A comparison of these results reveals that the contribution of the higher-than-three-body MB interactions is always attractive and non-negligible even at such a large separation, in contrast to common assumptions. The procedure employed is quite general and is applicable, in principle, to any shape or size of dielectric cluster. We present numerical results for clusters composed of atoms with polarizability consistent with silica, for which the higher-than-three-body MB correction term can be as high as 42% of the atomic pairwise sum. This result is quite sensitive to the anisotropy and orientation of the cluster, in contrast to the result found in the additive case. We also present a power law expansion of the total van der Waals interaction as a series of n-body interaction terms.     

Electronic structure and chemical bond in naphthalene and anthracene

We investigated the electronic structure of crystalline naphthalene and anthracene within the framework of density functional theory including van der Waals interactions (DFT-D). It is established that for better agreement with experimental values it is necessary to use the increased values of the van der Waals radii, which is caused by an overestimated value of the van der Waals interactions in crystalline linear oligoacenes. Utilization of the DFT-D leads to a correct account of the dispersion forces, which results in a high precision of the computed lattice parameters and cohesive energy. Based on the relaxed crystal structures, we have computed the total and deformation electron density and determined the mechanism of chemical bonds formation in crystals of naphthalene and anthracene. It has been established that the chemical bond in molecular crystals is formed under the influence of not only intramolecular but also intermolecular interactions. On the basis of the Mulliken population analysis it was revealed that two C(3) atoms in naphthalene (or C(3) and C(4) in anthracene) have a positive charge and the population of the rest of the carbon atoms increased, as compared with isolated molecule.     

Design-atom approach for the quantum mechanical/molecular mechanical covalent boundary: a design-carbon atom with five valence electrons

A critical issue underlying the accuracy and applicability of the combined quantum mechanical/molecular mechanical (QM/MM) methods is how to describe the QM/MM boundary across covalent bonds. Inspired by the ab initio pseudopotential theory, here we introduce a novel design atom approach for a more fundamental and transparent treatment of this QM/MM covalent boundary problem. The main idea is to replace the boundary atom of the active part with a design atom, which has a different number of valence electrons but very similar atomic properties. By modifying the Troullier-Martins scheme, which has been widely employed to construct norm-conserving pseudopotentials for density functional calculations, we have successfully developed a design-carbon atom with five valence electrons. Tests on a series of molecules yield very good structural and energetic results and indicate its transferability in describing a variety of chemical bonds, including double and triple bonds.     

Geometry optimization using tuned and balanced redistributed charge schemes for combined quantum mechanical and molecular mechanical calculations

We performed geometry optimizations using the tuned and balanced redistributed charge algorithms to treat the QM-MM boundary in combined quantum mechanical and molecular mechanical (QM/MM) methods. In the tuned and balanced redistributed charge (TBRC) scheme, the QM boundary atom is terminated by a tuned F link atom, and the charge of the MM boundary atom is properly adjusted to conserve the total charge of the entire QM/MM system; then the adjusted MM boundary charge is moved evenly to the midpoints of the bonds between the MM boundary atom and its neighboring MM atoms. In the tuned and balanced redistributed charge-2 (TBRC2) scheme, the adjusted MM boundary charge is moved evenly to all MM atoms that are attached to the MM boundary atom. A new option, namely charge smearing, has been added to the TBRC scheme, yielding the tuned and balanced smeared redistributed charge (TBSRC) scheme. In the new scheme, the redistributed charges near the QM-MM boundary are smeared to make the electrostatic interactions between the QM region and the redistributed charges more realistic. The TBRC2 scheme and new TBSRC scheme have been tested for various kinds of bonds at a QM-MM boundary, including C-C, C-N, C-O, O-C, N-C, C-S, S-S, S-C, C-Si, and O-N bonds. Charge smearing is necessary if the redistributed charges are close to the QM region, as in the TBSRC scheme, but not if the redistributed charge is farther from the QM region, as in the TBRC2 scheme. We found that QM/MM results using either the TBRC2 scheme or the TBSRC scheme agree well with full QM results; the mean unsigned error (MUE) of the QM/MM deprotonation energy is 1.6 kcal/mol in both cases, and the MUE of QM/MM optimized bond lengths over the three bonds closest to the QM-MM boundary, with errors averaged over the protonated forms and unprotonated forms, is 0.015 ? for TBRC2 and 0.021 ? for TBSRC. The improvements in the new scheme are essential for QM-MM boundaries that pass through a polar bond, but even for boundaries that pass through C-C bonds, the improvement can be quite significant.     

Direct evaluation of individual hydrogen bond energy in situ in intra- and intermolecular multiple hydrogen bonds system

The results of evaluating the individual hydrogen bond (H-bond) strength are expected to be helpful for the rational design of new strategies for molecular recognition or supramolecular assemblies. Unfortunately, there is few obvious and unambiguous means of evaluating the energy of a single H-bond within a multiple H-bonds system. We present a local analytic model, ABEEMσπ H-bond energy (HBE) model based on ab initio calculations (MP2) as benchmark, to directly and rapidly evaluate the individual HBE in situ in inter- and intramolecular multiple H-bonds system. This model describes the HBE as the sum of electrostatic and van der Waals (vdW) interactions which all depend upon the geometry and environment, and the ambient environment of H-bond in the model is accounted fairly. Thus, it can fairly consider the cooperative effect and secondary effect. The application range of ABEEMσπ HBE model is rather wide. This work has discussed the individual H-bond in DNA base pair and protein peptide dimers. The results indicate that the interactions among donor H atom, acceptor atom as well as those atoms connected to them with 1,2 or 1,3 relationships are all important for evaluating the HBE, although the interaction between the donor H atom and the acceptor atom is large. Furthermore, our model quantitatively indicates the polarization ability of N, O, and S in a new style, and gives the percentage of the polarization effect in HBE, which can not be given by fixed partial charge force field.     

Specific and nonspecific interaction forces between Escherichia coli and silicon nitride, determined by poisson statistical analysis

The nature of the physical interactions between Escherichia coli JM109 and a model surface (silicon nitride) was investigated in water via atomic force microscopy (AFM). AFM force measurements on bacteria can represent the combined effects of van der Waals and electrostatic forces, hydrogen bonding, steric interactions, and perhaps ligand-receptor type bonds. It can be difficult to decouple these forces into their individual components since both specific (chemical or short-range forces such as hydrogen bonding) and nonspecific (long-range colloidal) forces may be present in the overall profiles. An analysis is presented based on the application of Poisson statistics to AFM adhesion data, to decouple the specific and nonspecific interactions. Comparisons with classical DLVO theory and a modified form of a van der Waals expression for rough surfaces were made in order to help explain the nature of the interactions. The only specific forces in the system were due to hydrogen bonding, which from the Poisson analysis were found to be -0.125 nN. The nonspecific forces of 0.155 nN represent an overall repulsive interaction. These nonspecific forces are comparable to the forces calculated from DLVO theory, in which electrostatic-double layer interactions are added to van der Waals attractions calculated at the distance of closest approach, as long as the van der Waals model for "rough" spherical surfaces is used. Calculated electrostatic-double layer and van der Waals interactions summed to 0.116 nN. In contrast, if the classic (i.e., smooth) sphere-sphere model was used to predict the van der Waals forces, the sum of electrostatic and van der Waals forces was -7.11 nN, which appears to be a large overprediction. The Poisson statistical analysis of adhesion forces may be very useful in applications of bacterial adhesion, because it represents an easy way to determine the magnitude of hydrogen bonding in a given system and it allows the fundamental forces to be easily broken into their components.     

原子的边界半径

本文建议和讨论2了原子大小的一种新量度-原子的边界半径, 经出了边界半径的周期表。对于惰性气体原子和汞原子, 有实验测得的有效半径, 它们与边界半径符合得相当好。原子的边界半径与实验的van der Waals半径有良好的线性关系。因此, 由边界半径可以预言某些原子的有效半径以及van der Waals半径。     

A transferable coarse-grained model for hydrogen-bonding liquids

We present here a recent development of a generalized coarse-grained model for use in molecular simulations. In this model, interactions between coarse-grained particles consist of both van der Waals and explicit electrostatic components. As a result, the coarse-grained model offers the transferability that is lacked by most current effective-potential based approaches. The previous center-of-mass framework (P. A. Golubkov and P. Ren, J. Chem. Phys., 2006, 125, 64103) is generalized here to include arbitrary off-center interaction sites for both Gay-Berne and multipoles. The new model has been applied to molecular dynamic simulations of neat methanol liquid. By placing a single point multipole at the oxygen atom rather than at the center of mass of methanol, there is a significant improvement in the ability to capture hydrogen-bonding. The critical issue of transferability of the coarse-grained model is verified on methanol-water mixtures, using parameters derived from neat liquids without any modification. The mixture density and internal energy from coarse-grained molecular dynamics simulations show good agreement with experimental measurements, on a par with what has been obtained from more detailed atomic models. By mapping the dynamics trajectory from the coarse-grained simulation into the all-atom counterpart, we are able to investigate atomic-level structure and interaction. Atomic radial distribution functions of neat methanol, neat water and mixtures compare favorably to experimental measurements. Furthermore, hydrogen-bonded 6- and 7-molecule chains of water and methanol observed in the mixture are in agreement with previous atomic simulations.     

Interaction Forces between Hydrophobic and Hydrophilic Self-Assembled Monolayers

An investigation is presented of the interaction of charged self-assembled monolayers (SAMs) with a monoprotic ionizable acid functional group (-COOH) and uncharged SAMs with a methyl terminated functional group (-CH(3)). The strength of the interactions are determined using an atomic force microscope. For all electrolyte conditions investigated the interactions are not well described by a summation of van der Waals attractions and electrostatic repulsions in a manner suggesting that van der Waals attractions are screened. The repulsions are accurately described as corresponding to two surfaces of different charge interacting with surface charges that are independent of separation (i.e., the constant charge model). A small adhesion force was observed under all conditions and its magnitude increased with NaCl concentration. Copyright 2000 Academic Press.     

van der Waals forces in presence of free charges: an exact derivation from equilibrium quantum correlations

We study interatomic forces in a fluid consisting of a mixture of free charges and neutral atoms in the framework of the quantum many-body problem at nonzero temperature and nonzero density. Of central interest is the interplay between van der Waals forces and screening effects due to free charges. The analysis is carried out in a partially recombined hydrogen plasma in the Saha regime. The effective potentials in the medium between two atoms, or an atom and a charge, or two charges, are determined from the large-distance behavior of equilibrium proton-proton correlations. We show, in a proper low-temperature and low-density scaling limit, that those potentials all decay as r(-6) at large distance r, while the corresponding amplitudes are calculated exactly. In particular, the presence of free charges only causes a partial (nonexponential) screening of the atomic potential, and it does not modify its typical r(-6) decay. That potential reduces to the standard van der Waals form for two atoms in vacuum when the temperature is driven to zero. The analysis is based on first principles: it does not assume preformed atoms and takes into account in a coherent way all effects, quantum mechanical binding, ionization, and collective screening, which originate from the Coulomb potential. Our method relies on the path integral representation of the quantum Coulomb gas.