CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations

A first-generation fluctuating charge (FQ) force field to be ultimately applied for protein simulations is presented. The electrostatic model parameters, the atomic hardnesses, and electronegativities, are parameterized by fitting to DFT-based charge responses of small molecules perturbed by a dipolar probe mimicking a water dipole. The nonbonded parameters for atoms based on the CHARMM atom-typing scheme are determined via simultaneously optimizing vacuum water-solute geometries and energies (for a set of small organic molecules) and condensed phase properties (densities and vaporization enthalpies) for pure bulk liquids. Vacuum solute-water geometries, specifically hydrogen bond distances, are fit to 0.19 A r.m.s. error, while dimerization energies are fit to 0.98 kcal/mol r.m.s. error. Properties of the liquids studied include bulk liquid structure and polarization. The FQ model does indeed show a condensed phase effect in the shifting of molecular dipole moments to higher values relative to the gas phase. The FQ liquids also appear to be more strongly associated, in the case of hydrogen bonding liquids, due to the enhanced dipolar interactions as evidenced by shifts toward lower energies in pair energy distributions. We present results from a short simulation of NMA in bulk TIP4P-FQ water as a step towards simulating solvated peptide/protein systems. As expected, there is a nontrivial dipole moment enhancement of the NMA (although the quantitative accuracy is difficult to assess). Furthermore, the distribution of dipole moments of water molecules in the vicinity of the solutes is shifted towards larger values by 0.1-0.2 Debye in keeping with previously reported work.     

An interpretation of the enhancement of the water dipole moment due to the presence of other water molecules

The dipole moment of the gas phase water monomer is 1.85 D. When solvated in bulk water, the dipole moment of an individual water molecule is observed to be enhanced to the much larger value of 2.9 +/- 0.6 D. To understand the origin of this dipole moment enhancement, the effective fragment potential (EFP) method is used to solvate an ab initio water molecule to predict the dipole moments for various cluster sizes. The dipole moment as a function of cluster size, nH 2O, is investigated [for n = 6-20 (even n), 26, 32, 41, and 50]. Localized charge distributions are used in conjunction with localized molecular orbitals to interpret the dipole moment enhancement. These calculations suggest that the enhancement of the dipole moment originates from the decrease of the angle between the dipole vectors of the lone pairs on oxygen as the number of hydrogen bonds to that oxygen increases. Thus, the decreased angle, and the consequent increase in water dipole moment, is most likely to occur in environments with a larger number of hydrogen bonds, such as the center of a cluster of water molecules.     

Boron substituted graphene: energy landscape for hydrogen adsorption

We have analyzed the modifications of interaction energy between a molecule of hydrogen and graphene layers partially substituted by boron. We show that the presence of boron modifies the symmetry of the energy landscape. It is due to both the larger boron size (with respect to carbon) and its stronger interaction with hydrogen molecules. The changes of energy surface are not confined to the neighborhood of substituted sites but extend over several graphene carbon sites, making the surface more heterogeneous. We show that the average increase of adsorption energy could meet DOE targets for hydrogen storage if a partial charge transfer between boron and hydrogen occurs during adsorption.     

Single dibenzoterrylene molecules in an anthracene crystal: main insertion sites.

We present a spectroscopic study of the properties of the two principal insertion sites (at 785.1 and 794.3 nm) of single dibenzoterrylene molecules in anthracene single crystals at cryogenic temperatures. We measured the temperature dependence of the line width, the orientation of the transition dipole moments, and the Stark effect. We performed molecular dynamics simulations, which show that one dibenzoterrylene molecule preferably replaces three anthracene molecules. From simulated annealing, we derive the molecular conformations in the most stable insertion sites and the orientations of the transition dipole moments. The good agreement between the spectroscopic results and the simulations allows us to propose unambiguous structures for the two principal spectroscopic sites.     

Isotope effect of hydrogen and lithium hydride molecules. Application of the dynamic extended molecular orbital method and energy component analysis

In order to explore the isotope effect including the nuclear–electronic coupling and nuclear quantum effects under the one-particle approximation, we apply the dynamic extended molecular orbital (DEMO) method and energy component analysis to the hydrogen and lithium hydride isotope molecules. Since the DEMO method determines both electronic and nuclear wave functions simultaneously by variationally optimizing all parameters embedded in the basis sets, the virial theorem is completely satisfied and guarantees the relation of the kinetic and potential energies. We confirm the isotope effect on internuclear distances, nuclear and electronic wave functions, dipole moment, the polarizability, and each energy component. In the case of isotopic species of the hydrogen molecule, the total energy decreases from the H₂ to the T₂ molecule due to the stabilization of the nuclear–electronic potential component, as well as the nuclear kinetic one. In the case of the lithium hydride molecule, the energy lowering by replacing ⁶Li with ⁷Li is calculated to be greater than that by replacing H with D. This is mainly caused by the small destabilization of electron–electron and nuclear–nuclear repulsion in ⁷LiH compared to ⁶LiH, while the change in the repulsive components from ⁶LiH to ⁶LiD increases. Received: 24 March 1999 / Accepted: 5 August 1999 / Published online: 15 December 1999     

外型-1,4-氧桥-环己基-2,3-二羧酸的晶体及分子结构

外型-1,4-氧桥-环己基-2,3-二羧酸晶体属单斜晶系,空间群为P2_1/n;晶胞参数为:α=5.594(3)A,b=11.178(7)A,c=14.675(11)A,β=91.46(5)°;Ζ=4.从直接法得到结构的初始模型,经块矩阵最小二乘修正后,最后的R值为0.072.在晶体中,分子间的O—H…O氢键将分子连接成层型氢键体系.使用自编的CNDO/2程序,计算得电子的能量、分子的总能量、偶极矩及各原子的电荷密度和净电荷.     

“Crystal” conformations of 2-methyl-2,4-pentanediol: Dipole moment calculations and molecular structure optimizations

The structures of eight symmetrically independent molecules of 2-methyl-2,4-pentanediol (MPD) in six crystal substances are studied based on the data retrieved from the Cambridge Structural Database (CSD). Coordinates of the most part of hydrogen atoms in MPD molecules were not determined experimentally or not presented in CSD, however, O...O distances provide the conclusion about the formation of intramolecular hydrogen bonds in four molecules. To perform quantum chemical calculations the absent hydrogen atoms were added. The choice of H atomic positions in hydroxyl groups are based on the analysis of possible formation of intra- and intermolecular hydrogen bonds by MPD molecules in the respective crystals. The DFT method with the B3PW91 functional and the 6-31G(d,p) basis set is used to carry out for the first time: 1) the calculation of dipole moments and energies for MPD molecules in “crystal” conformations; 2) the optimization of the structure of these molecules with the calculation of dipole moments for the conformations corresponding to the local energy minima. It is found that among the molecules with the experimental geometric parameters one of the conformations without intramolecular hydrogen bonds is most favorable (μ = 0.56 D). As a result of the energy minimization of eight “crystal” conformations in vacuum, five energetically different conformers are obtained. Among them the conformer with the intramolecular hydrogen bond has the lowest energy (μ = 3.53 D). Four variants of the molecular structure correspond to it in the considered crystals, out of which two are R-enantiomers and two S-enantiomers.     

Off‐atomic site charges in some anions,metal cations,and complexes: Significance for electrostatic properties and binding

Electronic structures and properties of several anions, metal cations, and their complexes with neutral molecules were investigated at the HF/6‐31G** and B3LYP/6‐31G** levels of theory. Charges shifted from atomic sites due to atomic orbital hybridization called hybridization displacement charges (HDC) were investigated in detail. It has been found that many components of HDC are associated with each atom of ion that are shifted from the atomic sites, those associated with metal cations being shifted by large distances as found previously in electrically neutral systems. It is shown that atomic orbitals are appreciably rehybridized in going from neutral molecules to anions and cations. Molecular dipole moments and surface molecular electrostatic potentials (MEP) are obtained satisfactorily using HDC for the various types of species mentioned above. In the OH^?? H₂O complex, reversal of direction of shift of an HDC component associated with the hydrogen atom of H₂O involved in hydrogen bonding, indicates that the hydrogen bond between OH^? and H₂O would have some covalent character. Other atomic site‐based point charge models cannot provide such information about the nature of bonding. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem 2007     

Structural Transformation of Surface-Confined Porphyrin Networks by Addition of Co Atoms

The self-assembly of a nickel-porphyrin derivative (Ni-DPPyP) containing two pyridyl coordinating sites and two pentyl chains at trans meso positions was studied with scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS) and low energy electron diffraction (LEED) on Au(111). Deposition of Ni-DPPyP onto Au(111) gave rise to a close-packed network for coverages smaller or equal to one monolayer as revealed by STM and LEED. The molecular arrangement of this two-dimensional network is stabilized via hydrogen bonds formed between the pyridyl's nitrogen and hydrogen atoms from the pyrrole groups of neighboring molecules. Subsequent deposition of cobalt atoms onto the close-packed network and post-deposition annealing at 423 K led to the formation of a Co-coordinated hexagonal porous network. As confirmed by XPS measurements, the porous network is stabilized by metal-ligand interactions between one cobalt atom and three pyridyl ligands, each pyridyl ligand coming from a different Ni-DPPyP molecule.     

Pyrene: hydrogenation, hydrogen evolution, and π-band model

We present a theoretical investigation of the hydrogenation of pyrene and of the subsequent molecular hydrogen evolution. Using density functional theory (DFT) at the GGA-PBE level, the chemical binding of atomic hydrogen to pyrene is found to be exothermic by up to 1.6 eV with a strong site dependence. The edge C atoms are found most reactive. The barrier for the formation of the hydrogen-pyrene bond is small, down to 0.06 eV. A second hydrogen binds barrierless at many sites. The most stable structure of dihydrogenpyrene is more stable by 0.64 eV than pyrene plus a molecular hydrogen molecule and a large barrier of 3.7 eV for the molecular hydrogen evolution is found. Using a simple tight-binding model we demonstrate that the projected density of π-states can be used to predict the most stable binding sites for hydrogen atoms and the model is used to investigate the most favorable binding sites on more hydrogenated pyrene molecules and on coronene. Some of the DFT calculations were complemented with hybrid-DFT (PBE0) showing a general agreement between the DFT and hybrid-DFT results.     

Energy of charged states in the RDX crystal: trapping of charge-transfer pairs as a possible mechanism for initiating detonation

Calculations for the crystalline energetic material RDX (1,3,5-trinitro-1,3,5-triazacyclohexane) yield the effective polarizability (17.2 angstroms3), local electric field tensor, effective dipole moment (9.40 D), and dipole-dipole energy (-27.2 kJ/mol). Fourier-transform techniques give the polarization energy P for a single charge in the perfect crystal as -1.14 eV; the charge-dipole energy W(D) is zero if the crystal carries no bulk dipole moment. Polarization energies for charge-transfer (CT) pairs combine with the Coulomb energy E(C) to give the screened Coulomb energy E(scr); screening is nearly isotropic with E(scr) approximately = E(C)2.6. For CT pairs W(D) reduces to a term deltaW(D) arising from the interaction of the charge on each ion with the change in dipole moment on the other ion relative to the neutral molecule. The dipole moments are calculated as 7.40 D for the neutral molecule and 6.84 D and 7.44 D for the anion and cation, giving the lowest two CT pairs at -1.34 eV and -0.94 eV. The changes in P and W(D) near a molecular vacancy yield traps with depths that reach 400 meV for single charges and 185 meV for the nearest-neighbor CT pair. Divacancies yield traps with depths nearly equal to the sum of those produced by the separate vacancies. These results are consistent with a mechanism in which detonation of RDX is initiated by mechanical generation of CT pairs that localize at vacancies, recombine, and release energy sufficient to break bonds; crystals of molecules with lower dipole moments should be less sensitive.     

Potential energy surfaces for the interaction of atomic and diatomic hydrogen with lithium metal clusters

In this paper a modified CNDO/2 method is used to study the interaction of hydrogen atoms and molecules with molecular clusters simulating the (100) surface of solid lithium metal. The modification, described in an earlier papers, involves rescaling bicentric CNDO/2 energy contributions with known diatomic bond energies. Potential energy curves are calculated for six attack points by the hydrogen atom on the surface, and for one attack point by the molecule. The results indicate that in both atom and molecule forms hydrogen penetrates the surface and that the molecule most likely dissociates.     

含羧酸镁(钙)官能团的多孔芳香骨架材料储氢性能的预测

用MP2方法,TZVPP基组以及基组重叠误差(BSSE)校正计算了氢分子与修饰在多孔芳香骨架(PAF)上的羧酸镁、羧酸钙官能团的相互作用,并建立了描述这一相互作用的分子力学力场.在此基础上用巨正则系综蒙特卡洛(GCMC)模拟预测了氢气在该种新型PAF材料上的吸附等温线.量子化学计算结果表明,每个羧酸镁、羧酸钙官能团分别可以提供13、14个氢分子吸附位点,与每个氢分子的平均结合能在8kJ·mol-1左右.通过比较不同温度和压力下材料的绝对吸附量和超额吸附量发现,在PAF骨架中引入羧酸镁、羧酸钙官能团可以显著提高材料的综合储氢性能,达到并超过了美国能源部提出的2015年储氢标准.同时该工作还揭示了氢吸附量与材料的表面积、空腔体积和分子作用强度间的复杂关系.     

Ab initio properties of Li-group-II molecules for ultracold matter studies

We perform a systematic investigation of the electronic properties of the (2)Σ(+) ground state of Li-alkaline-earth dimers. These molecules are proposed as possible candidates for quantum simulation of lattice-spin models. We apply powerful quantum chemistry coupled-cluster method and large basis sets to calculate potential energies and permanent dipole moments for the LiBe, LiMg, LiCa, LiSr, and LiYb molecules. Agreement of calculated molecular constants with existing experimental data is better than or equal to 8%. Our results reveal a surprising irregularity in the dissociation energy and bond length with an increase in the reduced mass of the molecule. At the same time, the permanent dipole moment at the equilibrium separation has the smallest value between 0.01 a.u. and 0.1 a.u. for the heaviest (LiSr and LiYb) molecules and increases to 1.4 a.u. for the lightest (LiBe), where 1 a.u. is one atomic unit of dipole moment. We consider our study of the (2)Σ(+) molecules a first step towards a comprehensive analysis of their interactions in an optical trap.     

Multimode calculations of rovibrational energies and dipole transition intensities for polyatomic molecules with torsional motion: application to H2O2

We report rigorous calculations of rovibrational energies and dipole transition intensities for hydrogen peroxide using a new version of MULTIMODE as applied to molecules with torsional (reaction path) motion. The key features which permit such calculations for moderately sized polyatomic molecules of this general type are briefly described. A previous, accurate potential energy surface and a new high-level ab initio dipole moment surface are employed in these calculations. Detailed comparisons are made with high-resolution experimental spectral intensities from the HITRAN database.     

Orientational motions of vibrational chromophores in molecules at the air/water interface with time-resolved sum frequency generation

The first time-resolved experiments in which interfacial molecules are pumped to excited electronic states and probed by vibrational sum frequency generation (SFG) are reported. This method was used to measure the out-of-plane rotation dynamics, i.e. time dependent changes in the polar angle, of a vibrational chromophore of an interfacial molecule. The chromophore is the carbonyl group, the rotation observed is that of the -C=O bond axis, with respect to the interfacial normal, and the interfacial molecule is coumarin 314 (C314) at the air/water interface. The orientational relaxation time was found to be 220+/-20 ps, which is much faster than the orientational relaxation time of the permanent dipole moment axis of C314 at the same interface, as obtained from pump-second harmonic probe experiments. Possible effects on the rotation of the -C=O bond axis due to the carbonyl group hydrogen bonding with interfacial water are discussed. From the measured equilibrium orientation of the permanent dipole moment axis and the carbonyl axis, and knowledge of their relative orientation in the molecule, the absolute orientation of C314 at the air/water interface is obtained.     

Fast 3D molecular superposition and similarity search in databases of flexible molecules

We present a new method (fFLASH) for the virtual screening of compound databases that is based on explicit three-dimensional molecular superpositions. fFLASH takes the torsional flexibility of the database molecules fully into account, and can deal with an arbitrary number of conformation-dependent molecular features. The method utilizes a fragmentation-reassembly approach which allows for an efficient sampling of the conformational space. A fast clique-based pattern matching algorithm generates alignments of pairs of adjacent molecular fragments on the rigid query molecule that are subsequently reassembled to complete database molecules. Using conventional molecular features (hydrogen bond donors and acceptors, charges, and hydrophobic groups) we show that fFLASH is able to rapidly produce accurate alignments of medium-sized drug-like molecules. Experiments with a test database containing a diverse set of 1780 drug-like molecules (including all conformers) have shown that average query processing times of the order of 0.1 seconds per molecule can be achieved on a PC.