The Experts below are selected from a list of 22206 Experts worldwide ranked by ideXlab platform

John Z. H. Zhang - One of the best experts on this subject based on the ideXlab platform.

  • A Fragment Quantum Mechanical Method for Metalloproteins.
    Journal of Chemical Theory and Computation, 2019
    Co-Authors: Tong Zhu, John Z. H. Zhang
    Abstract:

    An accurate energy calculation of metalloprotein is of crucial importance and also a theoretical challenge. In this work, a metal molecular fractionation with conjugate caps (metal-MFCC) approach is developed for efficient linear-scaling Quantum calculation of potential energy and atomic forces of metalloprotein. In this approach, the potential energy of a given protein is calculated by a linear combination of potential energies of the neighboring residues, two-body interaction energy between non-neighboring residues that are spatially in close contact and the potential energy of the metal binding group. The calculation of each fragment is embedded in a field of point charges representing the remaining protein environment. Numerical studies were carried out to check the performance of this Method, and the calculated potential energies and atomic forces all show excellent agreement with the full system calculations at the M06-2X/6-31G(d) level. By combining the energy calculation with molecular dynamic sim...

  • Fragment Quantum Mechanical Method for Large-Sized Ion-Water Clusters.
    Journal of Chemical Theory and Computation, 2017
    Co-Authors: Jinfeng Liu, John Z. H. Zhang
    Abstract:

    Fragmentation Methods have been widely studied for computing Quantum Mechanical (QM) energy of medium-sized water clusters, but less attention has been paid to large-sized ion–water clusters, in which many-body QM interaction is more significant, because of the charge-transfer effect between ions and water molecules. In this study, we utilized electrostatically embedded generalized molecular fractionation (EE-GMF) Method for full QM calculation of the large-sized ion–water clusters (up to 15 Na+ and 15 Cl– ions solvated with 119 water molecules). Through systematic validation using different fragment sizes, we show that, by using distance thresholds of 6 A for both the two-body and three-body QM interactions, the EE-GMF Method is capable of providing accurate ground-state energies of large-sized ion–water clusters at different ab initio levels (including HF, B3LYP, M06-2X, and MP2) with significantly reduced computational cost. The deviations of EE-GMF from full system calculations are within a few kcal/m...

  • calculation of protein ligand binding affinities based on a fragment Quantum Mechanical Method
    RSC Advances, 2015
    Co-Authors: Jinfeng Liu, John Z. H. Zhang, Xianwei Wang
    Abstract:

    An electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) Method (J. Phys. Chem. A, 2013, 117, 7149) has been successfully used for efficient linear-scaling Quantum Mechanical (QM) calculations of protein energies. Furthermore, an efficient approach that combined the EE-GMFCC Method with a conductor-like polarizable continuum model (CPCM), termed as EE-GMFCC-CPCM (J. Chem. Phys., 2013, 139, 214104), was developed for ab initio calculations of the electrostatic solvation energy of proteins. In this study, we applied the EE-GMFCC-CPCM Method for the calculation of binding affinities of 14 avidin–biotin analogues. The calculation delineated the contributions of interaction energy and electrostatic solvation energy to the binding affinity. The binding affinity of each ligand bound to avidin was calculated at the HF/6-31G* and B3LYP/6-31G* levels with empirical dispersion corrections, respectively. The correlation coefficient (R) between the calculated binding energies and experimental values is 0.75 at the HF/6-31G*-D level based on single complex structure calculations, as compared to 0.73 of the force field result. On the other hand, the correlation coefficient between the calculated binding energies and the experimental values is 0.85 at the B3LYP/6-31G*-D level based on single complex structure calculations, and this correlation can be further improved to 0.88 when multiple snapshots are considered. Our study demonstrates that the EE-GMFCC-CPCM Method is capable of providing reliable predictions of binding affinities for various ligands bound to the same target.

  • Calculation of protein–ligand binding affinities based on a fragment Quantum Mechanical Method
    RSC Advances, 2015
    Co-Authors: Jinfeng Liu, Xianwei Wang, John Z. H. Zhang
    Abstract:

    An electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) Method (J. Phys. Chem. A, 2013, 117, 7149) has been successfully used for efficient linear-scaling Quantum Mechanical (QM) calculations of protein energies. Furthermore, an efficient approach that combined the EE-GMFCC Method with a conductor-like polarizable continuum model (CPCM), termed as EE-GMFCC-CPCM (J. Chem. Phys., 2013, 139, 214104), was developed for ab initio calculations of the electrostatic solvation energy of proteins. In this study, we applied the EE-GMFCC-CPCM Method for the calculation of binding affinities of 14 avidin–biotin analogues. The calculation delineated the contributions of interaction energy and electrostatic solvation energy to the binding affinity. The binding affinity of each ligand bound to avidin was calculated at the HF/6-31G* and B3LYP/6-31G* levels with empirical dispersion corrections, respectively. The correlation coefficient (R) between the calculated binding energies and experimental values is 0.75 at the HF/6-31G*-D level based on single complex structure calculations, as compared to 0.73 of the force field result. On the other hand, the correlation coefficient between the calculated binding energies and the experimental values is 0.85 at the B3LYP/6-31G*-D level based on single complex structure calculations, and this correlation can be further improved to 0.88 when multiple snapshots are considered. Our study demonstrates that the EE-GMFCC-CPCM Method is capable of providing reliable predictions of binding affinities for various ligands bound to the same target.

  • an improved fragment based Quantum Mechanical Method for calculation of electrostatic solvation energy of proteins
    Journal of Chemical Physics, 2013
    Co-Authors: Xiangyu Jia, John Z. H. Zhang, Jinfeng Liu, Xianwei Wang, Ye Mei
    Abstract:

    An efficient approach that combines the electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) Method with conductor-like polarizable continuum model (CPCM), termed EE-GMFCC-CPCM, is developed for ab initio calculation of the electrostatic solvation energy of proteins. Compared with the previous MFCC-CPCM study [Y. Mei, C. G. Ji, and J. Z. H. Zhang, J. Chem. Phys. 125, 094906 (2006)], Quantum Mechanical (QM) calculation is applied to deal with short-range non-neighboring interactions replacing the classical treatment. Numerical studies are carried out for proteins up to 3837 atoms at the HF/6-31G* level. As compared to standard full system CPCM calculations, EE-GMFCC-CPCM shows clear improvement over the MFCC-CPCM Method for both the total electrostatic solvation energy and its components (the polarized solute-solvent reaction field energy and wavefunction distortion energy of the solute). For large proteins with 1000–4000 atoms, where the standard full system ab ini...

Zhiyong Xie - One of the best experts on this subject based on the ideXlab platform.

  • structure of graphene and Mechanical and bonding characteristics of single wall carbon nanotube by linear scaling Quantum Mechanical Method
    Journal of Materials Science & Technology, 2010
    Co-Authors: Jun Cai, Chongyu Wang, Zhiyong Xie
    Abstract:

    Using a linear scaling self-consistent-charge density functional tight binding (SCC-DFTB) and an ab initio Dmol Method, the bonding characteristics and Young's modulus of (10, 0) and (10,10) single-walled carbon nanotubes are calculated. The structure of a graphene is also calculated. It is found that the C-C and C-H bond length, their distribution characteristics on the tube, and Young's modulus of the tube by linear scaling SCC-DFTB are identical to those by ab initio, while the computing cost by the linear scaling SCC-DFTB is reduced by more than 30 times as compared with that by the Dmol for the (10,0) and (10,10) tubes By computing the structure of a graphene it is also found that the linear scaling SCCDFTB is reliable and time-saving.

Lasse Jensen - One of the best experts on this subject based on the ideXlab platform.

  • a discrete interaction model Quantum Mechanical Method for simulating plasmon enhanced two photon absorption
    Journal of Chemical Theory and Computation, 2018
    Co-Authors: Lasse Jensen
    Abstract:

    In this work, we extend the discrete interaction model/Quantum Mechanical (DIM/QM) Method to simulate plasmon-enhanced two-photon absorption (PETPA). The metal nanoparticle is treated atomistically by means of electrodynamics, while the molecule is described using damped cubic response theory within a time-dependent density functional theory framework. Using DIM/QM, we study the PETPA of para-nitroaniline (p-NA) with a focus on the local and image field effects, the molecular orientation effects, and the molecule–nanoparticle distance effects. Our findings show that the enhancement is more complex than the simple |E|4 enhancement mechanism, where |E| is the local field at the position of the molecule. Because of specific interactions with the nanoparticle, we find that a TPA dark state of p-NA can be significantly enhanced through a coupling with the plasmon excitation. The results presented in this work illustrate that the coupling between molecular excitations and plasmons can give rise to unusual and c...

  • a discrete interaction model Quantum Mechanical Method for simulating nonlinear optical properties of molecules near metal surfaces
    Molecular Physics, 2013
    Co-Authors: John M Rinaldi, Seth M Morton, Lasse Jensen
    Abstract:

    In this work, we extend the discrete interaction model/Quantum mechanics (DIM/QM) Method to calculate the frequency-dependent hyperpolarisabilities of molecules near metal surfaces. The DIM/QM Method is a polarisable Quantum mechanics/molecular mechanics Method, which represents the metal surface atomistically and thus allows for explicitly modelling the influence of the local environment on the optical properties of a molecule. The interactions between the metal surface and the molecules include both the image field and local field effects. The image field effects arise from the response induced in the metal surface due to the molecule’s electronic charge distributions whereas the local field effects arise from interactions between the metal surface and the external light. The frequency-dependent first-hyperpolarisability is obtained in an efficient way based on time-dependent density functional theory and the (2n+1) rule. The Method was tested for calculating the first-hyperpolarisability responsible fo...

  • a discrete interaction model Quantum Mechanical Method for simulating surface enhanced raman spectroscopy
    Journal of Chemical Physics, 2012
    Co-Authors: John L Payton, Seth M Morton, Justin E Moore, Lasse Jensen
    Abstract:

    We have derived and implemented analytical gradients for the discrete interaction model/Quantum mechanics (DIM/QM) Method. DIM/QM combines an atomistic electrodynamics model with time-dependent density functional theory and thus enables modeling of the optical properties for a molecule while taking into account the local environment of a nanoparticle's surface. The DIM/QM analytical gradients allow for geometry optimizations, vibrational frequencies, and Raman spectra to be simulated for molecules interacting with metal nanoparticles. We have simulated the surface-enhanced Raman scattering (SERS) spectra for pyridine adsorbed on different sites of icosahedral nanoparticles with diameters between 1 and 8 nm. To describe the adsorption of the pyridine molecule onto the metal surface, we have implemented a coordination-dependent force field to differentiate the various local surface environments. We find that the DIM/QM Method predicts geometries and frequencies that are in good agreement with full QM simula...

  • a discrete interaction model Quantum Mechanical Method to describe the interaction of metal nanoparticles and molecular absorption
    Journal of Chemical Physics, 2011
    Co-Authors: Seth M Morton, Lasse Jensen
    Abstract:

    A frequency-dependent Quantum mechanics/molecular mechanics Method for the calculation of response properties of molecules adsorbed on metal nanoparticles is presented. This discrete interaction model/Quantum mechanics (DIM/QM) Method represents the nanoparticle atomistically, thus accounting for the local environment of the nanoparticle surface on the optical properties of the adsorbed molecule. Using the DIM/QM Method, we investigate the coupling between the absorption of a silver nanoparticle and of a substituted naphthoquinone. This system is chosen since it shows strong coupling due to a molecular absorption peak that overlaps with the plasmon excitation in the metal nanoparticle. We show that there is a strong dependence not only on the distance of the molecule from the metal nanoparticle but also on its orientation relative to the nanoparticle. We find that when the transition dipole moment of an excitation is oriented towards the nanoparticle there is a significant increase in the molecular absorp...

  • a discrete interaction model Quantum Mechanical Method for describing response properties of molecules adsorbed on metal nanoparticles
    Journal of Chemical Physics, 2010
    Co-Authors: Seth M Morton, Lasse Jensen
    Abstract:

    A new polarizable Quantum mechanics/molecular mechanics Method for the calculation of response properties of molecules adsorbed on metal nanoparticles is presented. This Method, which we denote the discrete interaction model/Quantum mechanics (DIM/QM) Method, represents the nanoparticle atomistically which enables the modeling of the influence of the local environment of a nanoparticle surface on the optical properties of a molecule. Using DIM/QM, we investigate the excitation energies of rhodamine-6G (R6G) and crystal violet (CV) adsorbed on silver and gold nanoparticles of different quasispherical shapes and sizes. The metal nanoparticle is characterized by its static total polarizability, a reasonable approximation for frequencies far from the plasmon resonance. We observe that for both R6G and CV, the presence of the nanoparticle shifts the strongest excitation to the red ∼40 nm and also increases the oscillator strength of that excitation. The shifts in excitation energies due to the nanoparticle sur...

Jinfeng Liu - One of the best experts on this subject based on the ideXlab platform.

  • prediction of excited state properties of oligoacene crystals using fragment based Quantum Mechanical Method
    Journal of Physical Chemistry A, 2019
    Co-Authors: Jinfeng Liu, Haitao Sun, William J Glover
    Abstract:

    A fundamental understanding of the excited-state properties of molecular crystals is of central importance for their optoelectronics applications. In this study, we developed the electrostatically ...

  • accurate prediction of energetic properties of ionic liquid clusters using a fragment based Quantum Mechanical Method
    Physical Chemistry Chemical Physics, 2017
    Co-Authors: Jinfeng Liu
    Abstract:

    Accurate prediction of physicochemical properties of ionic liquids (ILs) is of great significance to understand and design novel ILs with unique properties. This study employed the electrostatically embedded generalized molecular fractionation (EE-GMF) Method for accurate energy calculation of IL clusters. The accuracy and efficiency of the EE-GMF Method are systematically assessed at different ab initio levels (including HF, DFT and MP2) with diverse basis sets. With the fixed charge model for the embedding field, the deviations of the EE-GMF approach from conventional full system calculations are within 2.58 kcal mol-1 for all IL clusters with up to 30 ion pairs (720 atoms), tested in this study. Moreover, this linear-scaling fragment Quantum Mechanical (QM) Method can significantly reduce the total computational cost for post-HF Methods. The EE-GMF approach is well-suited for studying the energetic, structural and dynamical properties of ILs using high-level ab initio theories.

  • Fragment Quantum Mechanical Method for Large-Sized Ion-Water Clusters.
    Journal of Chemical Theory and Computation, 2017
    Co-Authors: Jinfeng Liu, John Z. H. Zhang
    Abstract:

    Fragmentation Methods have been widely studied for computing Quantum Mechanical (QM) energy of medium-sized water clusters, but less attention has been paid to large-sized ion–water clusters, in which many-body QM interaction is more significant, because of the charge-transfer effect between ions and water molecules. In this study, we utilized electrostatically embedded generalized molecular fractionation (EE-GMF) Method for full QM calculation of the large-sized ion–water clusters (up to 15 Na+ and 15 Cl– ions solvated with 119 water molecules). Through systematic validation using different fragment sizes, we show that, by using distance thresholds of 6 A for both the two-body and three-body QM interactions, the EE-GMF Method is capable of providing accurate ground-state energies of large-sized ion–water clusters at different ab initio levels (including HF, B3LYP, M06-2X, and MP2) with significantly reduced computational cost. The deviations of EE-GMF from full system calculations are within a few kcal/m...

  • calculation of protein ligand binding affinities based on a fragment Quantum Mechanical Method
    RSC Advances, 2015
    Co-Authors: Jinfeng Liu, John Z. H. Zhang, Xianwei Wang
    Abstract:

    An electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) Method (J. Phys. Chem. A, 2013, 117, 7149) has been successfully used for efficient linear-scaling Quantum Mechanical (QM) calculations of protein energies. Furthermore, an efficient approach that combined the EE-GMFCC Method with a conductor-like polarizable continuum model (CPCM), termed as EE-GMFCC-CPCM (J. Chem. Phys., 2013, 139, 214104), was developed for ab initio calculations of the electrostatic solvation energy of proteins. In this study, we applied the EE-GMFCC-CPCM Method for the calculation of binding affinities of 14 avidin–biotin analogues. The calculation delineated the contributions of interaction energy and electrostatic solvation energy to the binding affinity. The binding affinity of each ligand bound to avidin was calculated at the HF/6-31G* and B3LYP/6-31G* levels with empirical dispersion corrections, respectively. The correlation coefficient (R) between the calculated binding energies and experimental values is 0.75 at the HF/6-31G*-D level based on single complex structure calculations, as compared to 0.73 of the force field result. On the other hand, the correlation coefficient between the calculated binding energies and the experimental values is 0.85 at the B3LYP/6-31G*-D level based on single complex structure calculations, and this correlation can be further improved to 0.88 when multiple snapshots are considered. Our study demonstrates that the EE-GMFCC-CPCM Method is capable of providing reliable predictions of binding affinities for various ligands bound to the same target.

  • Calculation of protein–ligand binding affinities based on a fragment Quantum Mechanical Method
    RSC Advances, 2015
    Co-Authors: Jinfeng Liu, Xianwei Wang, John Z. H. Zhang
    Abstract:

    An electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) Method (J. Phys. Chem. A, 2013, 117, 7149) has been successfully used for efficient linear-scaling Quantum Mechanical (QM) calculations of protein energies. Furthermore, an efficient approach that combined the EE-GMFCC Method with a conductor-like polarizable continuum model (CPCM), termed as EE-GMFCC-CPCM (J. Chem. Phys., 2013, 139, 214104), was developed for ab initio calculations of the electrostatic solvation energy of proteins. In this study, we applied the EE-GMFCC-CPCM Method for the calculation of binding affinities of 14 avidin–biotin analogues. The calculation delineated the contributions of interaction energy and electrostatic solvation energy to the binding affinity. The binding affinity of each ligand bound to avidin was calculated at the HF/6-31G* and B3LYP/6-31G* levels with empirical dispersion corrections, respectively. The correlation coefficient (R) between the calculated binding energies and experimental values is 0.75 at the HF/6-31G*-D level based on single complex structure calculations, as compared to 0.73 of the force field result. On the other hand, the correlation coefficient between the calculated binding energies and the experimental values is 0.85 at the B3LYP/6-31G*-D level based on single complex structure calculations, and this correlation can be further improved to 0.88 when multiple snapshots are considered. Our study demonstrates that the EE-GMFCC-CPCM Method is capable of providing reliable predictions of binding affinities for various ligands bound to the same target.

Jun Cai - One of the best experts on this subject based on the ideXlab platform.

  • structure of graphene and Mechanical and bonding characteristics of single wall carbon nanotube by linear scaling Quantum Mechanical Method
    Journal of Materials Science & Technology, 2010
    Co-Authors: Jun Cai, Chongyu Wang, Zhiyong Xie
    Abstract:

    Using a linear scaling self-consistent-charge density functional tight binding (SCC-DFTB) and an ab initio Dmol Method, the bonding characteristics and Young's modulus of (10, 0) and (10,10) single-walled carbon nanotubes are calculated. The structure of a graphene is also calculated. It is found that the C-C and C-H bond length, their distribution characteristics on the tube, and Young's modulus of the tube by linear scaling SCC-DFTB are identical to those by ab initio, while the computing cost by the linear scaling SCC-DFTB is reduced by more than 30 times as compared with that by the Dmol for the (10,0) and (10,10) tubes By computing the structure of a graphene it is also found that the linear scaling SCCDFTB is reliable and time-saving.

  • effect of ending surface on energy and young s modulus of single walled carbon nanotubes studied using linear scaling Quantum Mechanical Method
    Physica B-condensed Matter, 2009
    Co-Authors: Jun Cai, Yan Wang, Chenying Wang
    Abstract:

    Abstract By using a linear scaling self-consistent charge, density functional tight-binding (SCC-DFTB) Method and an ab intio Dmol3 calculation, the energy and Young's modulus as a function of tube length for (10, 0) single-walled carbon nanotubes (SWCNTs) are investigated. It was found that with increasing the length of SWCNTs the Young's modulus increases rapidly, then, there is a slow increase, which ultimately approaches a constant value after the length is increased to ~20 nm, whereas a reversed variation tendency was found for the average energy of atoms in SWCNTs with a change of the tube length. We found that the characters of the length-dependent energy and Young's modulus stem from the changed Py-DOS of atoms in the ending region of the tube. Here one simple formula is proposed for quantitatively explaining the length-dependent energy and modulus.