Effect of quantum partial charges on the structure and dynamics of water in single-walled carbon nanotubes

In this work, using quantum partial charges, computed from 6-31G(**)B3LYP density functional theory, in molecular dynamics simulations, we found that water inside (6,6) and (10,0) single-walled carbon nanotubes with similar diameters but with different chiralities has remarkably different structural and dynamical properties. Density functional calculations indicate that tubes with different chiralities have significantly different partial charges at the ends of tubes. The partial charges at the ends of a (10,0) tube are around 4.5 times higher than those of a (6,6) tube. Molecular dynamics simulations with the partial charges show different water dipole orientations. In the (10,0) tube, dipole vectors of water molecules at the end of the tube point towards the water reservoir resulting in the formation of an L defect in the center region. This is not observed in the (6,6) tube where dipole vectors of all the water molecules inside the tube point towards either the top or the bottom water reservoir. The water diffusion coefficient is found to increase in the presence of the partial charges. Water in the partially charged (10,0) tube has a lower diffusion coefficient compared to that of in the partially charged (6,6) tube.     

Building molecular charge distributions from fragments: Application to HIV-1 protease inhibitors

Interaction energies are a function of the molecular charge distribution. In previous work, we found that the set of atomic partial charges giving the best agreement with experimental vacuum dipole moments were from density functional theory calculations using an extended basis set. Extension of such computations to larger molecules requires an atomic partial charge calculation beyond present computational resources. A solution to this problem is the calculation of atomic partial charges for segments of the molecule and reassociation of such fragments to yield partial charges for the entire molecule. Various partitions and reassociation methods for five molecules relevant to HIV-1 protease inhibitors are examined. A useful method of reassociation is introduced in which atomic partial charges for a large molecule are computed by fitting to the combined electrostatic potential calculated from the fragment partial charges. As expected, the best sites for partitions are shown to be carbon—carbon rather than carbon—nitrogen bonds. © 1997 by John Wiley & Sons, Inc.     

DFT Study of Physisorption Effect of the Curcumin on CNT(8,0-6) Nanotube for Biological Applications

In the given work the adsorption properties of molecule curcumin((1 E,6 E)-1,7-bis(4-hydroxy-3-methoxyphenyl)-1,6-heptadiene-3,5-dione) on CNT(8,0-6) nanotube were investigated by the density functional theory(DFT) in the solvent water for the first time. The non-bonded interaction effects of compounds curcumin and CNT(8,0-6) nanotube on the electronic properties, UV/Vis spectra, chemical shift tensors and natural charges were determined and discussed. The electronic spectra of the compound curcumin and the complex CNT(8,0-6)/curcumin in the solvent water were calculated by time dependent density functional theory(TD-DFT) for investigation of the maximum wavelength value of molecule Curcumin before and after the non-bonded interaction with the CNT(8,0-6) nanotube and molecular orbitals involved in the formation of absorption spectrum of the complex CNT(8,0-6)/curcumin at maximum wavelength.     

Encapsulation effect of π-conjugated quaterthiophene on the radial breathing and tangential modes of semiconducting and metallic single-walled carbon nanotubes

We developed a hybrid approach, combining the density functional theory, molecular mechanics, bond polarizability model and the spectral moment's method to compute the nonresonant Raman spectra of a single quaterthiophene (4T) molecule encapsulated into a single-walled carbon nanotube (metallic or semiconducting). We reported the optimal tube diameter allowing the 4T encapsulation. The influence of the encapsulation on the Raman modes of the 4T molecule and those of the nanotube (radial breathing modes and tangential modes) are analyzed. An eventual charge transfer between the 4T oligomer and the nanotube is discussed.     

Various atomic charge calculation schemes of CoMFA on HIF‐1 inhibitors of moracin analogs

Selection of appropriate partial charges in a molecule is crucial to derive good quantitative structure–activity relationship models. In this work, several partial atomic charges were assigned and tested in a comparative molecular field analysis (CoMFA) models. Many CoMFA models were generated for a series of hypoxia inducible factor 1 (HIF‐1) inhibitors using various partial atomic charges including charge equalization, Mülliken population analysis (MPA), natural population analysis, and electrostatic potential (ESP)‐derived charges. These atomic charges were investigated at various theoretical levels such as empirical, semiempirical, Hartree–Fock (HF), and density functional theory (DFT). Among them, Merz‐Singh‐Kollman (MK) ESP‐derived charges at the level of HF/6‐31G* gave the highest predictive q² with experimental pIC₅₀ values. With this charge scheme, a detailed analysis of CoMFA model was performed to understand the electrostatic interactions between ligand and receptor. More elaborate charge calculation schemes such as HF and DFT correlated more strongly with activity than empirical or semiempirical schemes. The choice of optimization methods was important. As geometries were fully optimized at the given levels of theory, the aligned structures were different. They differed considerably, especially for the flexible parts. This was likely the source of the substantial variation of q² values, even when the same steric factor was considered without electrostatic parameters. ESP‐derived charges were most appropriate to describe CoMFA electrostatic interactions among MPA, NBA, and ESP charges. Overall q² values vary considerably (0.8–0.5) depending on the charge schemes applied. The results demonstrate the need to consider more appropriate atomic charges rather than default CoMFA charges. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Accurate partial atomic charges for high-energy molecules using class IV charge models with the MIDI! basis set

We have recently developed a new class IV charge model for calculating partial atomic charges in molecules. The new model, called charge model 3 (CM3), was parameterized for calculations on molecules containing H, Li, C, N, O, F, Si, S, P, Cl, and Br by Hartree–Fock theory and by hybrid density functional theory (HDFT) based on the modified Perdew–Wang density functional with several basis sets. In the present article, we extend CM3 for calculating partial atomic charges by Hartree–Fock theory with the economical but well balanced MIDI! basis set. Then, using a test set of accurate dipole moments for molecules containing nitramine functional groups (which include many high-energy materials), we demonstrate the utility of several parameters designed to improve the charges in molecules containing both N and O atoms. We also show that one of our most recently developed CM3 models that is designed for use with wave functions calculated at the mPWXPW91/MIDI! level of theory (where X denotes a variable percentage of Hartree–Fock exchange) gives accurate charge distributions in nitramines without additional parameters for N and O. To demonstrate the reliability of partial atomic charges calculated with CM3, we use these atomic charges to calculate polarization free energies for several nitramines, including the commonly used explosives 1,3,5-trinitro-s-triazine (RDX) and 2,4,6,8,10,12-hexanitrohexaazaisowurtzitane (HNIW), in nitromethane. These polarization energies are large and negative, indicating that electrostatic interactions between the charge distribution of the molecule and the solvent make a large contribution to the free energy of solvation of nitramines. By extension, the same conclusion should apply to solid-state condensation. Also, in contrast to some other charge models, CM3 yields atomic charges that are relatively insensitive to the presence of buried atoms and small conformational changes in the molecule, as well as to the level of treatment of electron correlation. This type of charge model should be useful in the future development of solvation models and force fields designed to estimate intramolecular interactions of nitramines in the condensed phase.     

Quantum chemical study of electronic and structural properties of retinal and some aromatic analogs

The electronic and structural properties of retinal and four analogs were studied using semiempirical, ab initio Hartree-Fock, and density functional theory methods with the aim to evaluate the effects caused by some structural modifications in the ring bound to the polyenic chain and compared with the all-E-trans-retinal molecule. Therefore, some properties such as bond lengths, bond angles, atomic charges derived from electrostatic potential charges from electrostatic potential using grid based method as well as frontier orbitals of the polyenic chain were analyzed. Furthermore, the transition energies of the molecules were also calculated using the Zerner's intermediate neglect of differential overlap-spectroscopic, time-dependent Hartree-Fock, and time-dependent density functional theory methods. The results indicate that in spite of the structural modifications of retinal derivatives in comparison with all-E-trans-retinal, their properties seem similar. Thus, these molecules may behave similarly to all-E-trans-retinal and possibly be attempted in the search of novel molecular devices.     

椅型碳纳米管吸附氧原子的密度泛函理论研究

利用密度泛函B3LYP对有限长扶手椅形单壁碳纳米管(3,3),(4,4)和(5,5)吸附O原子的几何结构、电子属性、反应能和红外光谱进行了系统地理论研究,获得了一些有意义的结果,主要包括如下4个方面:(1)2个O原子吸附在管外壁垂直于管轴的C—C键形成开环的轮烯结构,吸附在管内壁形成环氧结构;(2)O原子吸附在管外壁要比吸附在管内壁具有较大的能隙和吸附反应能;(3)与单壁碳纳米管管外壁吸附1个O原子相比,2个O原子吸附在管外壁具有较大的吸附反应能;(4)B3LYP得到的C—O伸缩振动频率与实验一致.     

Theoretical Prediction of Adsorption Properties of Carmustine Drug on Various Sites of the Outer Surface of the Single-Walled Boron Nitride Nanotube and Investigation of Urea Effect on Drug Delivery by DFT and MD

In this work, the adsorption behavior of Carmustine (BCNU) drug over the (6,0) zigzag single-wall boron nitride nanotube (SWBNNT) is studied by means of density functional theory calculations and molecular dynamics simulations (MD). The calculated adsorption energies proved that the adsorption of BCNU molecule on SWBNNT is a physisorption process. The natural bond orbital calculations demonstrated that existence of a charge transfer from the SWBNNT to the BCNU molecule. Moreover, quantum theory of atoms in molecules showed that the hydrogen bonds and electrostatic interactions are two major factors contributed to the overall stabilities of the complexes. Furthermore, interaction of BCNU with the surface of single wall BNNT at 310 K and 1 bar in the present of water and different concentration of Urea molecules has been studied by MD simulation. The MD results confirm that the highest number of hydrogen bond and the lowest value of Lennard-Jones (L-J) energy between nanotube and drug exist in the simulation system with concentration of 1 mol L^?1 Urea.     

Oxygen gas-induced lip-lip interactions on a double-walled carbon nanotube edge

We have investigated adsorption of an O(2) molecule on a double-walled carbon nanotube (DWCNT) edge using density functional theory calculations. An O(2) molecule adsorbs exothermally without an adsorption barrier at open nanotube edges that are energetically favorable with a large adsorption energy of about -9 eV in most cases. Dissociative adsorption of an O(2) molecule induces various spontaneous lip-lip interactions via the bridged carbon atoms, generating the closed tube ends. This explains why the DWCNTs are chemically more stable than the single-walled nanotubes during observed field emission experiments. The field emission takes place via the localized states of the bridged carbon atoms, not via those of the adsorbed oxygen atoms particularly in the armchair nanotubes. We also find that some O(2) precursor states exist as a bridge between tube edges.     

A new method to evaluate the stability of the covalent compound: by the charges on the common atom or group

A new method of comparing and analyzing the electrostatic potential (ESP) charges of the common atom or group to evaluate and compare the stabilities of covalent compounds was introduced. That is, covalent compounds will become more stable when the electron acceptors accept adequate electrons and possess adequate negative charges, and the electron donors donate adequate electrons and possess adequate positive charges accordingly. All calculations were performed by density functional theory (DFT) and the general gradient approximation (GGA) method with the Beck-LYP hybrid functional and the DNP basis set in Acceryls' code Dmol3. Calculation results verified the method considering the molecular structure is well applied in the covalent molecule systems of hydrides, oxides, alkyl radicals, and nitro compounds. Furthermore, the method has good operability, for the charges can be easily obtained by simple calculation.     

Electrostatic and covalent contributions in the coordination bonds of transition metal complexes

To develop a molecular mechanics force field for modeling complexes of transition metals and organic ligands, the electrostatic and covalent contributions in the coordination bonds were investigated using quantum mechanical density functional theory and model complexes of glyoxal diimine and the 2+ cations of the first row transition metals. The VDD and Hirshfeld charges are found to be closely correlated with the extent of the electron transfer between the ligands and the cations. Assuming the electrostatic contribution can be represented by the atomic partial charges, the covalent contributions in the coordination bonds are estimated to be in a range of 54-92% for the systems calculated. A simple force field was parametrized to validate the partial charge representation.     

DFT study on the adsorption and dissociation of hydrogen sulfide on MgO nanotube

The adsorption of a H₂S molecule on the surface of an MgO nanotube was investigated using density functional theory. It was found that H₂S molecule can be associatively adsorbed on the tube surface without any energy barrier or it can be dissociated into –H and –SH species overcoming energy barrier of 4.03–7.77 kcal/mol. The associative adsorption is site selective so that the molecule is oriented in such a way that the sulfur atom was linked to an Mg atom. The HOMO–LUMO energy gap of the tube has slightly changed upon associative adsorption, while they were significantly influenced by dissociation process. Especially, the highest occupied molecular orbital of the tube shifts to higher energies which can facilitate electron emission current from the tube surface. Also, energy gap of the tube dramatically decreased by about 0.93–1.05 eV which influences the electrical conductivity of the tube.     

<Emphasis Type="Italic">Ab initio</Emphasis> study of the structure and electronic properties of magnesium and calcium nitrates and their crystal hydrates

The crystal structures and electronic properties of magnesium and calcium nitrates, magnesium nitrate hexahydrate, and calcium nitrate tetrahydrate are studied at the density functional theory level by a hybrid functional in the basis set of localized atomic orbitals using the CRYSTAL14 program code. Atomic structural parameters, atomic charges, bond populations, energy and electron spatial distributions are calculated. The mainly electrostatic nature of interactions between nitro groups and water molecules is shown. The spectrum of the density of states of crystal hydrates, in comparison with nitrates, contains additional bands due to the presence of water. In the spectra of unoccupied states a gap is observed: the anionic gap is ~6.5 eV and the cationic gap is ~8.8 eV.     

Theoretical studies on structures and aromaticity of finite-length armchair carbon nanotubes

[structure: see text] Depending on the exact length of the tube, the chemical structure of finite-length armchair [n,n] single-wall carbon nanotube (n = 5 and 6) falls into three different classes that may be referred to as Kekulé, incomplete Clar, and complete Clar networks. The C-C bond lengths, nucleus-independent chemical shift analysis, and orbital energies suggest that the chemical reactivities of the finite-length tube change periodically as the tube length is elongated by one-by-one layering of cyclic carbon array.     

DFT study of the dissociative adsorption of HF on an AlN nanotube

We have investigated the adsorption of hydrogen fluoride (HF) on the AlN nanotube surface using density functional theory in terms of energetic, structural and electronic properties. By overcoming energy barriers of 27.90–52.30 kcal/mol, HF molecule is dissociated into H and F species on the tube surface and its molecular structure is not preserved after the adsorption process. Dissociation energies have been calculated to be −52.57 and −70.10 kcal/mol. The process has negligible effect on the electronic and field emission properties of the AlN nanotube. This process may increase the solubility of AlN nanotubes.     

Extended treatment of charge response kernel comprising the density functional theory and charge regulation procedures

We propose an extended treatment of the charge response kernel (CRK), (partial differential Q(a)/partial differential V(b)), which describes the response of partial charges on atomic sites to external electrostatic potential, on the basis of the density functional theory (DFT) via the coupled perturbed Kohn-Sham equations. The present CRK theory incorporates regulation procedures in the definition of partial charges to avoid unphysical large fluctuation of the CRK on "buried" sites. The CRKs of some alcohol and organic molecules, methanol, ethanol, propanol, butanol, dimethylsulfoxide (DMSO), and tetrahydrofuran (THF) were calculated, demonstrating that the new CRK model at the DFT level has greatly improved the performance of accuracy in comparison with that at the Hartree-Fock level previously proposed. The CRK model was also applied to investigate spatial nonlocality of the charge response through alkyl chain sequences. The CRK model at the DFT level enables us to construct a nonempirical strategy for polarizable molecular modeling, with practical reliability and robustness.     

Effect of charge distribution on electrostatic chromophore—protein interactions in Bacteriorhodopsin

Charge distributions of a protonated and unprotonated Schiff base model compound are determined using different quantum chemical methods. After fitting the model molecule onto the protonated retinal Schiff base in Bacteriorhodopsin, electrostatic interaction energies between the model molecule and protein are calculated. Interaction energies as well as the calculated pK_1/2 values of the model molecule are shown to depend considerably on the chosen charge distribution. Electrostatic potential derived partial charges determined at different ab initio levels reveal interaction energies between the model molecule and nearby residues such as ARG-82, ASP-85, and ASP-212, which are relatively method independent. Consequently, such charge distributions also result in pK_1/2 values for the model molecule that are very similar. Larger deviations in the electrostatic interaction energies, however, are found in the case of charge distributions derived according to the Mulliken population analysis. Nevertheless, some sets of Mulliken derived partial charges predicted pK_1/2 values for the model molecule that are close to those determined with electrostatic potential derived partial charges. This agreement, however, is only achieved because the individual errors of the contributing terms are approximately compensated. The use of the extended atom model is shown to be problematic. Although potential derived charges can correctly describe electrostatic interaction energies, they fail to predict pK_1/2 values. On the basis of the present investigation a new set of partial charges for the protonated and unprotonated retinal Schiff base is proposed to be used in molecular dynamics simulations and electrostatics calculations. © 1997 by John Wiley & Sons, Inc.     

A new force field model for the simulation of transport properties of imidazolium-based ionic liquids

A new, non-polarizable force field model (FFM) for imidazolium-based, room-temperature ionic liquids (RTILs), 1-ethyl-3-methyl-imidazolium tetrafluoroborate and 1-butyl-3-methyl-imidazolium tetrafluoroborate, has been developed. Modifying the FFM originally designed by Liu et al. (J. Phys. Chem. B, 2004, 108, 12978-12989), the electrostatic charges on interacting sites are refined according to partial charges calculated by explicit-ion density functional theory. The refined FFM reproduces experimental heats of vaporization, diffusion coefficients, ionic conductivities, and shear viscosities of RTILs, which is a significant improvement over the original model (Zh. Liu, Sh. Huang and W. Wang, J. Phys. Chem. B, 2004, 108, 12978-12989). The advantages of the proposed procedure include clarity, simplicity, and flexibility. Expanding the functionality of our FFM conveniently only requires modification of the electrostatic charges. Our FFM can be extended to other classes of RTILs as well as condensed matter systems in which the ionic interaction requires an account of polarization effects.