Published in J Phys Chem B on June 11, 2008
Density functional tight binding: values of semi-empirical methods in an ab initio era. Phys Chem Chem Phys (2014) 0.89
Full-electron calculation of effective electronic couplings and excitation energies of charge transfer states: Application to hole transfer in DNA pi-stacks. J Chem Phys (2009) 0.86
First principles effective electronic couplings for hole transfer in natural and size-expanded DNA. J Phys Chem B (2009) 0.81
Perspective: Quantum mechanical methods in biochemistry and biophysics. J Chem Phys (2016) 0.78
A hybrid approach to simulation of electron transfer in complex molecular systems. J R Soc Interface (2013) 0.78
A combined DFT/Green's function study on electrical conductivity through DNA duplex between Au electrodes. Chem Phys Lett (2009) 0.77
Fragment-based Quantum Mechanical/Molecular Mechanical Simulations of Thermodynamic and Kinetic Process of the Ru(2+)-Ru(3+) Self-Exchange Electron Transfer. J Chem Theory Comput (2012) 0.77
Electronic parameters for charge transfer along DNA. Eur Phys J E Soft Matter (2010) 0.76
Biological applications of hybrid quantum mechanics/molecular mechanics calculation. J Biomed Biotechnol (2012) 0.75
The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure. J Mol Biol (2004) 7.38
Conversion of channelrhodopsin into a light-gated chloride channel. Science (2014) 2.56
Microbial and animal rhodopsins: structures, functions, and molecular mechanisms. Chem Rev (2013) 1.93
Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes. J Phys Chem B (2006) 1.83
Extension of the self-consistent-charge density-functional tight-binding method: third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction. J Phys Chem A (2007) 1.44
Color tuning in rhodopsins: the mechanism for the spectral shift between bacteriorhodopsin and sensory rhodopsin II. J Am Chem Soc (2006) 1.43
DFTB3: Extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB). J Chem Theory Comput (2012) 1.40
Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package. J Phys Chem A (2007) 1.27
Electronic structure of single DNA molecules resolved by transverse scanning tunnelling spectroscopy. Nat Mater (2007) 1.22
Mechanism of primary proton transfer in bacteriorhodopsin. Structure (2004) 1.17
Contact dependence of carrier injection in carbon nanotubes: an ab initio study. Phys Rev Lett (2006) 1.14
Three-dimensional printing of hierarchical and tough mesoporous bioactive glass scaffolds with a controllable pore architecture, excellent mechanical strength and mineralization ability. Acta Biomater (2011) 1.13
Dynamic and electronic transport properties of DNA translocation through graphene nanopores. Nano Lett (2013) 1.12
Room temperature in situ growth of B/BOx nanowires and BOx nanotubes. Nano Lett (2014) 1.10
Simulating water with the self-consistent-charge density functional tight binding method: from molecular clusters to the liquid state. J Phys Chem A (2007) 1.09
"Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis. J Am Chem Soc (2006) 1.09
Control of thermal and electronic transport in defect-engineered graphene nanoribbons. ACS Nano (2011) 1.04
Organic Zener diodes: tunneling across the gap in organic semiconductor materials. Nano Lett (2010) 1.04
Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer. Phys Chem Chem Phys (2005) 1.04
Description of phosphate hydrolysis reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) theory. 1. Parameterization. J Chem Theory Comput (2008) 1.03
Direct low-temperature nanographene CVD synthesis over a dielectric insulator. ACS Nano (2010) 1.01
Key role of electrostatic interactions in bacteriorhodopsin proton transfer. J Am Chem Soc (2004) 1.00
Validation of the density-functional based tight-binding approximation method for the calculation of reaction energies and other data. J Chem Phys (2005) 0.98
Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin. Proc Natl Acad Sci U S A (2008) 0.98
Tuning the conductance of a molecular switch. Nat Nanotechnol (2007) 0.94
Fuel-free locomotion of Janus motors: magnetically induced thermophoresis. ACS Nano (2013) 0.94
11-cis-retinal protonated Schiff base: influence of the protein environment on the geometry of the rhodopsin chromophore. Biochemistry (2002) 0.94
Filament depolymerization by motor molecules. Phys Rev Lett (2005) 0.94
Automatized parametrization of SCC-DFTB repulsive potentials: application to hydrocarbons. J Phys Chem A (2009) 0.93
Nonadiabatic QM/MM simulations of fast charge transfer in Escherichia coli DNA photolyase. J Phys Chem B (2011) 0.92
What governs the charge transfer in DNA? The role of DNA conformation and environment. J Phys Chem B (2008) 0.91
Application of the SCC-DFTB method to neutral and protonated water clusters and bulk water. J Phys Chem B (2011) 0.90
Towards an understanding of channelrhodopsin function: simulations lead to novel insights of the channel mechanism. J Mol Biol (2013) 0.90
Density functional tight binding: values of semi-empirical methods in an ab initio era. Phys Chem Chem Phys (2014) 0.89
Solvent fluctuations drive the hole transfer in DNA: a mixed quantum-classical study. J Phys Chem B (2009) 0.89
Effect of polarization on the opsin shift in rhodopsins. 1. A combined QM/QM/MM model for bacteriorhodopsin and pharaonis sensory rhodopsin II. J Phys Chem B (2008) 0.89
Bioactive SrO-SiO2 glass with well-ordered mesopores: characterization, physiochemistry and biological properties. Acta Biomater (2010) 0.89
Parameterization of the DFTB3 method for Br, Ca, Cl, F, I, K, and Na in organic and biological systems. J Chem Theory Comput (2015) 0.88
Structural model of channelrhodopsin. J Biol Chem (2012) 0.88
Effect of polarization on the opsin shift in rhodopsins. 2. Empirical polarization models for proteins. J Phys Chem B (2008) 0.88
Multifunctional magnetic mesoporous bioactive glass scaffolds with a hierarchical pore structure. Acta Biomater (2011) 0.88
Magnetofluidic platform for multidimensional magnetic and optical barcoding of droplets. Lab Chip (2015) 0.87
Magnetoresistive emulsion analyzer. Sci Rep (2013) 0.87
CVD-grown horizontally aligned single-walled carbon nanotubes: synthesis routes and growth mechanisms. Small (2012) 0.87
Peptide-lipid interactions of the stress-response peptide TisB that induces bacterial persistence. Biophys J (2012) 0.86
Solvent reorganization energy of hole transfer in DNA. J Phys Chem B (2009) 0.86
Proton storage site in bacteriorhodopsin: new insights from quantum mechanics/molecular mechanics simulations of microscopic pK(a) and infrared spectra. J Am Chem Soc (2011) 0.85
Selection of a DNA aptamer against norovirus capsid protein VP1. FEMS Microbiol Lett (2014) 0.84
A bottom-up route to enhance thermoelectric figures of merit in graphene nanoribbons. Sci Rep (2013) 0.84
Long-distance proton transfer with a break in the bacteriorhodopsin active site. J Am Chem Soc (2009) 0.84
Investigating the outskirts of Fe and Co catalyst particles in alumina-supported catalytic CVD carbon nanotube growth. ACS Nano (2010) 0.84
Controlled stability of molecular junctions. Angew Chem Int Ed Engl (2009) 0.84
Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications. Chem Rev (2016) 0.84
Charge transfer in model peptides: obtaining Marcus parameters from molecular simulation. J Phys Chem B (2012) 0.84
Extended polarization in third-order SCC-DFTB from chemical-potential equalization. J Phys Chem A (2012) 0.83
Combined density functional theory and Landauer approach for hole transfer in DNA along classical molecular dynamics trajectories. J Chem Phys (2009) 0.83
A modified QM/MM Hamiltonian with the Self-Consistent-Charge Density-Functional-Tight-Binding Theory for highly charged QM regions. J Chem Theory Comput (2012) 0.83
Atomistic modeling of mechanical properties of polycrystalline graphene. Nanotechnology (2014) 0.83
Control over Janus micromotors by the strength of a magnetic field. Nanoscale (2013) 0.83
Computational study of synthetic agonist ligands of ionotropic glutamate receptors. PLoS One (2013) 0.82
Graphene on Au(111): a highly conductive material with excellent adsorption properties for high-resolution bio/nanodetection and identification. Chemphyschem (2010) 0.82
Structural stability versus conformational sampling in biomolecular systems: why is the charge transfer efficiency in G4-DNA better than in double-stranded DNA? J Chem Phys (2010) 0.82
Organometallic complexes of graphene: toward atomic spintronics using a graphene web. ACS Nano (2011) 0.82
Efficient algorithms for the simulation of non-adiabatic electron transfer in complex molecular systems: application to DNA. Phys Chem Chem Phys (2013) 0.81
Solvent driving force ensures fast formation of a persistent and well-separated radical pair in plant cryptochrome. J Am Chem Soc (2015) 0.81
Phonon engineering in carbon nanotubes by controlling defect concentration. Nano Lett (2011) 0.81
Multiscale modeling of thermal conductivity of polycrystalline graphene sheets. Nanoscale (2014) 0.81
Suppression of the back proton-transfer from Asp85 to the retinal Schiff base in bacteriorhodopsin: a theoretical analysis of structural elements. J Struct Biol (2006) 0.81
Application of the computationally efficient self-consistent-charge density-functional tight-binding method to magnesium-containing molecules. J Phys Chem A (2007) 0.81
Graphene: Piecing it together. Adv Mater (2011) 0.81
Toward a reversible isolation of a C20 fullerene inside a tetraureacalix[4]arene dimer. A theoretical study. J Phys Chem A (2006) 0.80
Computational photochemistry of retinal proteins. J Comput Aided Mol Des (2006) 0.80
Coarse-grained time-dependent density functional simulation of charge transfer in complex systems: application to hole transfer in DNA. J Phys Chem B (2010) 0.80
Molecular simulation of water and hydration effects in different environments: challenges and developments for DFTB based models. J Phys Chem B (2014) 0.80
Guanosine-based hydrogen-bonded 2D scaffolds: metal-free formation of G-quartet and G-ribbon architectures at the solid/liquid interface. Chem Commun (Camb) (2015) 0.80
Parametrization of DFTB3/3OB for magnesium and zinc for chemical and biological applications. J Phys Chem B (2014) 0.80
Patterned biochemical functionalization improves aptamer-based detection of unlabeled thrombin in a sandwich assay. ACS Appl Mater Interfaces (2013) 0.80
Charge transport in desolvated DNA. J Chem Phys (2013) 0.79
The protonation state of Glu181 in rhodopsin revisited: interpretation of experimental data on the basis of QM/MM calculations. J Phys Chem B (2010) 0.79
Synthesis of carbon nanotubes with and without catalyst particles. Nanoscale Res Lett (2011) 0.79
Role of Arg82 in the early steps of the bacteriorhodopsin proton-pumping cycle. J Phys Chem B (2011) 0.79
Binding of hydroxyquinoline probes to human serum albumin: combining molecular modeling and Förster's resonance energy transfer spectroscopy to understand flexible ligand binding. J Phys Chem B (2013) 0.79
A hybrid approach to simulation of electron transfer in complex molecular systems. J R Soc Interface (2013) 0.78
A parabolic model to control quantum interference in T-shaped molecular junctions. Phys Chem Chem Phys (2013) 0.78
Anomalous conductance response of DNA wires under stretching. Nano Lett (2008) 0.78
QM/MM simulations of vibrational spectra of bacteriorhodopsin and channelrhodopsin-2. Phys Chem Chem Phys (2013) 0.78
Charge carrier mobilities in organic semiconductors: crystal engineering and the importance of molecular contacts. Phys Chem Chem Phys (2015) 0.78
Tuning the formation of discrete coordination nanostructures. Chem Commun (Camb) (2015) 0.77
Improved electronic properties from third-order SCC-DFTB with cost efficient post-SCF extensions. J Phys Chem A (2012) 0.77
Relativistic parametrization of the self-consistent-charge density-functional tight-binding method. 1. Atomic wave functions and energies. J Phys Chem A (2007) 0.77
Charge transfer in E. coli DNA photolyase: understanding polarization and stabilization effects via QM/MM simulations. J Phys Chem B (2013) 0.77
Excitation energies of a water-bridged twisted retinal structure in the bacteriorhodopsin proton pump: a theoretical investigation. Phys Chem Chem Phys (2013) 0.76
Color tuning in binding pocket models of the chlamydomonas-type channelrhodopsins. J Phys Chem B (2011) 0.76