Density functional based tight binding (DFTB) model is employed to study the sp3-to-sp2 transformation of diamond-like carbon at elevated temperatures. The understanding could lead to the direct-growth of graphene on ...Density functional based tight binding (DFTB) model is employed to study the sp3-to-sp2 transformation of diamond-like carbon at elevated temperatures. The understanding could lead to the direct-growth of graphene on a wide variety of substrates.展开更多
Molecular simulation finds application in a wide range of research fields based on life and materials sciences.It helps comprehend and predict the chemical and physical properties of substances;thus,it is useful in di...Molecular simulation finds application in a wide range of research fields based on life and materials sciences.It helps comprehend and predict the chemical and physical properties of substances;thus,it is useful in directing R&D and industrial production.In this special issue,we focus on molecular simulations in material sciences.Molecular simulation employs computational models from microscopic to mesoscopic levels,which is reflected in this special issue.For example,Liu et al.1 reported modulation of catalytic activity for CO2 hydrogenation using quantum density functional theory(DFT).Yin et al.2 parameterized a semiempirical density functional tight-binding(DFTB)model to study deposition of carbon on copper surface.At the atomic level,Ren et al.展开更多
Chemical modification and vertical stacking of two-dimensional materials are promising techniques for new nanoelectronic devices. We present Density Functional Tight Binding(DFTB) calculations of a field-effect device...Chemical modification and vertical stacking of two-dimensional materials are promising techniques for new nanoelectronic devices. We present Density Functional Tight Binding(DFTB) calculations of a field-effect device,based on lateral and vertical heterostructures of 2D materials. The device consists of a phosphorene channel protected by graphene sheets, which work as contacts and are divided into the source and drain by local hydrogenation of graphene, which gives insulating graphane. In this device composed of only 3 layers, single sheets of graphene-graphane can work as both leads and oxide gate, while also acting as protective layers for a phosphorene channel. We show how for perfect vd W heterostructures of graphane/phosphorene/graphane and graphene/phosphorene/graphene the Schottky barrier is deeply influenced by normal electric fields, and we characterize electronic transport of such a device. Finally, we characterize phosphorene channel doping and defects, which, at very high densities in the transport direction, enables transport inside the phosphorene bandgap.展开更多
In this paper we have designed a biosensor device built from B-N substituted graphene nanoribbon within density functional based tight-binding (DFTB) framework. We have investigated the interaction of the nucleobases ...In this paper we have designed a biosensor device built from B-N substituted graphene nanoribbon within density functional based tight-binding (DFTB) framework. We have investigated the interaction of the nucleobases adenine (A), Guanine (G), Cytosine (C) and Thymine (T) with device. Our calculation suggests that all the nucleobases have different interaction strength when they interact with device and shows that guanine has stronger interaction with device than other nucleobases. It reveals that the absorption energy shows the hierarchy: G > C > T > A. Our results also demonstrate the transport properties of the device and how the transport properties change due to the absorption of nucleobases on the device.展开更多
Defects in materials significantly alter their electronic and structural properties,which affect the per-formance of electronic devices,structural alloys,and functional materials.However,calculating all the possible d...Defects in materials significantly alter their electronic and structural properties,which affect the per-formance of electronic devices,structural alloys,and functional materials.However,calculating all the possible defects in complex materials with conventional Density Functional Theory(DFT)can be compu-tationally prohibitive.To enhance the efficiency of these calculations,we interfaced Density Functional Tight Binding(DFTB)with the Clusters Approach to Statistical Mechanics(CASM)software package for the first time.Using SiC and ZnO as representative examples,we show that DFTB gives accurate results and can be used as an efficient computational approach for calculating and pre-screening formation ener-gies/convex hulls.Our DFTB+CASM implementation allows for an efficient exploration(up to an order of magnitude faster than DFT)of formation energies and convex hulls,which researchers can use to probe other complex systems.展开更多
Despite the uniquely high thermal conductivity of graphene is well known,the exploitation of graphene into thermally conductive nanomaterials and devices is limited by the inefficiency of thermal contacts between the ...Despite the uniquely high thermal conductivity of graphene is well known,the exploitation of graphene into thermally conductive nanomaterials and devices is limited by the inefficiency of thermal contacts between the individual nanosheets.A fascinating yet experimentally challenging route to enhance thermal conductance at contacts between graphene nanosheets is through molecular junctions,allowing covalently connecting nanosheets,otherwise interacting only via weak Van der Waals forces.Beside the bare existence of covalent connections,the choice of molecular structures to be used as thermal junctions should be guided by their vibrational properties,in terms of phonon transfer through the molecular junction.In this paper,density functional tight-binding combined with Green's functions formalism was applied for the calculation of thermal conductance and phonon spectra of several different aliphatic and aromatic molecular junctions between graphene nanosheets.Effects of molecular junction length,conformation,and aromaticity were studied in detail and correlated with phonon tunnelling spectra.The theoretical insight provided by this work can guide future experimental studies to select suitable molecular junctions,in order to enhance the thermal transport by suppressing the interfacial thermal resistances.This is attractive for various systems,including graphene nanopapers and graphene polymer nanocomposites,as well as related devices.In a broader view,the possibility to design molecular junctions to control phonon transport currently appears as an efficient way to produce phononic devices and controlling heat management in nanostructures.展开更多
The interactions of formaldehyde(HCHO)molecule with S-doped anatase TiO_(2)(001)surface without and with water and oxygen were studied by density functional theory(DFT).The adsorption energy of HCHO adsorption on S-do...The interactions of formaldehyde(HCHO)molecule with S-doped anatase TiO_(2)(001)surface without and with water and oxygen were studied by density functional theory(DFT).The adsorption energy of HCHO adsorption on S-doped TiO_(2) surface with water and oxygen(-709.62 kJ/mol)is much larger than that without water and oxygen(-312.14 kJ/mol).For HCHO adsorption system without water and oxygen,one CeH bond of HCHO molecule is broken.The oxygen and carbon atoms of HCHO are bonded to the titanium and sulfur atoms of SeTiO_(2) surface,respectively,and form a CH_(2)OS structure.For the system with water and oxygen,H_(2)O and HCHO molecules are both dissociated.HCHO molecule not only interacts with TiO_(2) surface,but also combines with O_(2) molecule.Two CeH bonds of HCHO are broken,one hydrogen atom(H1)is bonded to the sulfur atom(S)of TiO_(2) surface doping,while another hydrogen atom(H_(2))is bonded to the O atom(O_(2))of O_(2) molecule.The remaining CeO bond can be oxidized to form CO_(2) in subsequent action by oxygen from the atmosphere.The surface doping of sulfur have significant impact on the degradation of HCHO molecule on anatase TiO_(2)(001)surface with H_(2)O and O_(2).展开更多
Motivated by several long-lasting mechanistic questions for biomolecular proton pumps,we have engaged in developing hybrid quantum mechanical/molecular mechanical(QM/MM) methods that allow an efficient and reliable de...Motivated by several long-lasting mechanistic questions for biomolecular proton pumps,we have engaged in developing hybrid quantum mechanical/molecular mechanical(QM/MM) methods that allow an efficient and reliable description of long-range proton transport in transmembrane proteins.In this review,we briefly discuss several relevant issues:the need to develop a "multi-scale" generalized solvent boundary potential(GSBP) for the analysis of chemical events in large trans-membrane proteins,approaches to validate such a protocol,and the importance of improving the flexibility of QM/MM Hamiltonian.Several recent studies of model and realistic protein systems are also discussed to help put the discussions into context.Collectively,these studies suggest that the QM/MM-GSBP framework based on an approximate density functional theory(SCC-DFTB) as QM holds the promise to strike the proper balance between computational efficiency,accuracy and generality.With additional improvements in the methodology and recent developments by others,especially powerful sampling techniques,this "multi-scale" framework will be able to help unlock the secrets of proton pumps and other biomolecular machines.展开更多
Motivated by several long-lasting mechanistic questions for biomolecular proton pumps,we have engaged in developing hybrid quantum mechanical/molecular mechanical(QM/MM) methods that allow an efficient and reliable de...Motivated by several long-lasting mechanistic questions for biomolecular proton pumps,we have engaged in developing hybrid quantum mechanical/molecular mechanical(QM/MM) methods that allow an efficient and reliable description of long-range proton transport in transmembrane proteins.In this review,we briefly discuss several relevant issues:the need to develop a "multi-scale" generalized solvent boundary potential(GSBP) for the analysis of chemical events in large trans-membrane proteins,approaches to validate such a protocol,and the importance of improving the flexibility of QM/MM Hamiltonian.Several recent studies of model and realistic protein systems are also discussed to help put the discussions into context.Collectively,these studies suggest that the QM/MM-GSBP framework based on an approximate density functional theory(SCC-DFTB) as QM holds the promise to strike the proper balance between computational efficiency,accuracy and generality.With additional improvements in the methodology and recent developments by others,especially powerful sampling techniques,this "multi-scale" framework will be able to help unlock the secrets of proton pumps and other biomolecular machines.展开更多
基金The project was supported by National Natural Science Foundation of China(21573201)the Ministry of Science and Technology of China(2016YFA0200604)and the Special Program for Applied Research on Super Computation of the National Nature Science Foundation of China-Guangdong Joint Fund(U1501501)~~
文摘Density functional based tight binding (DFTB) model is employed to study the sp3-to-sp2 transformation of diamond-like carbon at elevated temperatures. The understanding could lead to the direct-growth of graphene on a wide variety of substrates.
文摘Molecular simulation finds application in a wide range of research fields based on life and materials sciences.It helps comprehend and predict the chemical and physical properties of substances;thus,it is useful in directing R&D and industrial production.In this special issue,we focus on molecular simulations in material sciences.Molecular simulation employs computational models from microscopic to mesoscopic levels,which is reflected in this special issue.For example,Liu et al.1 reported modulation of catalytic activity for CO2 hydrogenation using quantum density functional theory(DFT).Yin et al.2 parameterized a semiempirical density functional tight-binding(DFTB)model to study deposition of carbon on copper surface.At the atomic level,Ren et al.
基金supported through the German Research Foundation within the project “Straintronics of imperfect quasi-two-dimensional materials: coplanar vs lamellar heterostructures” (CU 44/43).
文摘Chemical modification and vertical stacking of two-dimensional materials are promising techniques for new nanoelectronic devices. We present Density Functional Tight Binding(DFTB) calculations of a field-effect device,based on lateral and vertical heterostructures of 2D materials. The device consists of a phosphorene channel protected by graphene sheets, which work as contacts and are divided into the source and drain by local hydrogenation of graphene, which gives insulating graphane. In this device composed of only 3 layers, single sheets of graphene-graphane can work as both leads and oxide gate, while also acting as protective layers for a phosphorene channel. We show how for perfect vd W heterostructures of graphane/phosphorene/graphane and graphene/phosphorene/graphene the Schottky barrier is deeply influenced by normal electric fields, and we characterize electronic transport of such a device. Finally, we characterize phosphorene channel doping and defects, which, at very high densities in the transport direction, enables transport inside the phosphorene bandgap.
文摘In this paper we have designed a biosensor device built from B-N substituted graphene nanoribbon within density functional based tight-binding (DFTB) framework. We have investigated the interaction of the nucleobases adenine (A), Guanine (G), Cytosine (C) and Thymine (T) with device. Our calculation suggests that all the nucleobases have different interaction strength when they interact with device and shows that guanine has stronger interaction with device than other nucleobases. It reveals that the absorption energy shows the hierarchy: G > C > T > A. Our results also demonstrate the transport properties of the device and how the transport properties change due to the absorption of nucleobases on the device.
基金supported by the U.S.Department of Energy,Na-tional Energy Technology Laboratory(NETL),under Award No.DE-FE0030582.
文摘Defects in materials significantly alter their electronic and structural properties,which affect the per-formance of electronic devices,structural alloys,and functional materials.However,calculating all the possible defects in complex materials with conventional Density Functional Theory(DFT)can be compu-tationally prohibitive.To enhance the efficiency of these calculations,we interfaced Density Functional Tight Binding(DFTB)with the Clusters Approach to Statistical Mechanics(CASM)software package for the first time.Using SiC and ZnO as representative examples,we show that DFTB gives accurate results and can be used as an efficient computational approach for calculating and pre-screening formation ener-gies/convex hulls.Our DFTB+CASM implementation allows for an efficient exploration(up to an order of magnitude faster than DFT)of formation energies and convex hulls,which researchers can use to probe other complex systems.
文摘Despite the uniquely high thermal conductivity of graphene is well known,the exploitation of graphene into thermally conductive nanomaterials and devices is limited by the inefficiency of thermal contacts between the individual nanosheets.A fascinating yet experimentally challenging route to enhance thermal conductance at contacts between graphene nanosheets is through molecular junctions,allowing covalently connecting nanosheets,otherwise interacting only via weak Van der Waals forces.Beside the bare existence of covalent connections,the choice of molecular structures to be used as thermal junctions should be guided by their vibrational properties,in terms of phonon transfer through the molecular junction.In this paper,density functional tight-binding combined with Green's functions formalism was applied for the calculation of thermal conductance and phonon spectra of several different aliphatic and aromatic molecular junctions between graphene nanosheets.Effects of molecular junction length,conformation,and aromaticity were studied in detail and correlated with phonon tunnelling spectra.The theoretical insight provided by this work can guide future experimental studies to select suitable molecular junctions,in order to enhance the thermal transport by suppressing the interfacial thermal resistances.This is attractive for various systems,including graphene nanopapers and graphene polymer nanocomposites,as well as related devices.In a broader view,the possibility to design molecular junctions to control phonon transport currently appears as an efficient way to produce phononic devices and controlling heat management in nanostructures.
基金supported by Guangxi Natural Science Foundation(No.2017GXNSFAA198247).
文摘The interactions of formaldehyde(HCHO)molecule with S-doped anatase TiO_(2)(001)surface without and with water and oxygen were studied by density functional theory(DFT).The adsorption energy of HCHO adsorption on S-doped TiO_(2) surface with water and oxygen(-709.62 kJ/mol)is much larger than that without water and oxygen(-312.14 kJ/mol).For HCHO adsorption system without water and oxygen,one CeH bond of HCHO molecule is broken.The oxygen and carbon atoms of HCHO are bonded to the titanium and sulfur atoms of SeTiO_(2) surface,respectively,and form a CH_(2)OS structure.For the system with water and oxygen,H_(2)O and HCHO molecules are both dissociated.HCHO molecule not only interacts with TiO_(2) surface,but also combines with O_(2) molecule.Two CeH bonds of HCHO are broken,one hydrogen atom(H1)is bonded to the sulfur atom(S)of TiO_(2) surface doping,while another hydrogen atom(H_(2))is bonded to the O atom(O_(2))of O_(2) molecule.The remaining CeO bond can be oxidized to form CO_(2) in subsequent action by oxygen from the atmosphere.The surface doping of sulfur have significant impact on the degradation of HCHO molecule on anatase TiO_(2)(001)surface with H_(2)O and O_(2).
基金supported in part by NIH grant R01-GM084028NSF grant CHE-0957285+1 种基金U.S.Department of Energy Genomics:GTL and Sci-DAC Programs (DEFG02-04ER25627)supported in part by the National Science Foundation through a major instrumentation grant (CHE-0840494)
文摘Motivated by several long-lasting mechanistic questions for biomolecular proton pumps,we have engaged in developing hybrid quantum mechanical/molecular mechanical(QM/MM) methods that allow an efficient and reliable description of long-range proton transport in transmembrane proteins.In this review,we briefly discuss several relevant issues:the need to develop a "multi-scale" generalized solvent boundary potential(GSBP) for the analysis of chemical events in large trans-membrane proteins,approaches to validate such a protocol,and the importance of improving the flexibility of QM/MM Hamiltonian.Several recent studies of model and realistic protein systems are also discussed to help put the discussions into context.Collectively,these studies suggest that the QM/MM-GSBP framework based on an approximate density functional theory(SCC-DFTB) as QM holds the promise to strike the proper balance between computational efficiency,accuracy and generality.With additional improvements in the methodology and recent developments by others,especially powerful sampling techniques,this "multi-scale" framework will be able to help unlock the secrets of proton pumps and other biomolecular machines.
文摘Motivated by several long-lasting mechanistic questions for biomolecular proton pumps,we have engaged in developing hybrid quantum mechanical/molecular mechanical(QM/MM) methods that allow an efficient and reliable description of long-range proton transport in transmembrane proteins.In this review,we briefly discuss several relevant issues:the need to develop a "multi-scale" generalized solvent boundary potential(GSBP) for the analysis of chemical events in large trans-membrane proteins,approaches to validate such a protocol,and the importance of improving the flexibility of QM/MM Hamiltonian.Several recent studies of model and realistic protein systems are also discussed to help put the discussions into context.Collectively,these studies suggest that the QM/MM-GSBP framework based on an approximate density functional theory(SCC-DFTB) as QM holds the promise to strike the proper balance between computational efficiency,accuracy and generality.With additional improvements in the methodology and recent developments by others,especially powerful sampling techniques,this "multi-scale" framework will be able to help unlock the secrets of proton pumps and other biomolecular machines.