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Volumn 10, Issue 4, 2014, Pages 1518-1537

Parameterization of DFTB3/3OB for sulfur and phosphorus for chemical and biological applications

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EID: 84898462014     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct401002w     Document Type: Article
Times cited : (300)

References (94)
  • 2
    • 8844275956 scopus 로고    scopus 로고
    • Sulfatase: Structure, mechanism, biological activity, inhibition and synthetic utility
    • Hanson, S. R.; Best, M. D.; Wong, C. H. Sulfatase: structure, mechanism, biological activity, inhibition and synthetic utility Angew. Chem., Int. Ed. 2004, 43, 5736-5763
    • (2004) Angew. Chem., Int. Ed. , vol.43 , pp. 5736-5763
    • Hanson, S.R.1    Best, M.D.2    Wong, C.H.3
  • 3
    • 7644219892 scopus 로고    scopus 로고
    • State of understanding of Nafion
    • Mauritz, K. A.; Moore, R. B. State of understanding of Nafion Chem. Rev. 2004, 104, 4535-4585
    • (2004) Chem. Rev. , vol.104 , pp. 4535-4585
    • Mauritz, K.A.1    Moore, R.B.2
  • 4
    • 33846219497 scopus 로고    scopus 로고
    • Functionalized acenes and heteroacenes for organic electronics
    • Anthony, J. E. Functionalized acenes and heteroacenes for organic electronics Chem. Rev. 2006, 106, 5028-5048
    • (2006) Chem. Rev. , vol.106 , pp. 5028-5048
    • Anthony, J.E.1
  • 5
    • 0023099216 scopus 로고
    • Why nature chose phosphates
    • Westheimer, F. H. Why nature chose phosphates Science 1987, 235, 1173-1178
    • (1987) Science , vol.235 , pp. 1173-1178
    • Westheimer, F.H.1
  • 6
    • 0018881742 scopus 로고
    • Enzyme catalyzed phosphoryl transfer reactions
    • Knowles, J. R. Enzyme catalyzed phosphoryl transfer reactions Annu. Rev. Biochem. 1980, 49, 877-919
    • (1980) Annu. Rev. Biochem. , vol.49 , pp. 877-919
    • Knowles, J.R.1
  • 7
    • 33748591572 scopus 로고    scopus 로고
    • Enzymatic mechanisms of phosphate and sulfate transfer
    • Cleland, W. W.; Hengge, A. C. Enzymatic mechanisms of phosphate and sulfate transfer Chem. Rev. 2006, 106, 3252-3278
    • (2006) Chem. Rev. , vol.106 , pp. 3252-3278
    • Cleland, W.W.1    Hengge, A.C.2
  • 8
    • 0029022018 scopus 로고
    • Mutations of Ras Genes in Human Tumors
    • Kiaris, H.; Spandidos, D. A. Mutations of Ras Genes in Human Tumors Int. J. Oncol. 1995, 7, 413-421
    • (1995) Int. J. Oncol. , vol.7 , pp. 413-421
    • Kiaris, H.1    Spandidos, D.A.2
  • 9
    • 34248591612 scopus 로고    scopus 로고
    • Targeting the Raf-MEK-ERK mitogen-activated protein kinase cascade for the treatment of cancer
    • Roberts, P. J.; Der, C. J. Targeting the Raf-MEK-ERK mitogen-activated protein kinase cascade for the treatment of cancer Oncogene 2007, 26, 3291-3310
    • (2007) Oncogene , vol.26 , pp. 3291-3310
    • Roberts, P.J.1    Der, C.J.2
  • 10
    • 0036527429 scopus 로고    scopus 로고
    • Protein kinases - The major drug targets of the twenty-first century?
    • Cohen, P. Protein kinases-the major drug targets of the twenty-first century? Nat. Rev. Drug Discovery 2002, 1, 309-315
    • (2002) Nat. Rev. Drug Discovery , vol.1 , pp. 309-315
    • Cohen, P.1
  • 11
    • 0034306450 scopus 로고    scopus 로고
    • Specificity and mechanism of action of some commonly used protein kinase inhibitors
    • Davies, S. P.; Reddy, H.; Caivano, M.; Cohen, P. Specificity and mechanism of action of some commonly used protein kinase inhibitors Biochem. J. 2000, 351, 95-105
    • (2000) Biochem. J. , vol.351 , pp. 95-105
    • Davies, S.P.1    Reddy, H.2    Caivano, M.3    Cohen, P.4
  • 12
    • 0035904293 scopus 로고    scopus 로고
    • Rapamycin's resurrection: A new way to target the cancer cell cycle
    • Garber, K. Rapamycin's resurrection: A new way to target the cancer cell cycle J. Natl. Cancer Inst. 2001, 93, 1517-1519
    • (2001) J. Natl. Cancer Inst. , vol.93 , pp. 1517-1519
    • Garber, K.1
  • 13
    • 33751266159 scopus 로고    scopus 로고
    • Design and development of signal transduction inhibitors for cancer treatment: Experience and challenges with kinase targets
    • Collins, I.; Workman, P. Design and development of signal transduction inhibitors for cancer treatment: Experience and challenges with kinase targets Curr. Signal Transduction Ther. 2006, 1, 13-23
    • (2006) Curr. Signal Transduction Ther. , vol.1 , pp. 13-23
    • Collins, I.1    Workman, P.2
  • 14
    • 36549063511 scopus 로고    scopus 로고
    • Enzymes as a special class of therapeutic target: Clinical drugs and modes of action
    • Robertson, J. G. Enzymes as a special class of therapeutic target: clinical drugs and modes of action Curr. Opin. Struct. Biol. 2007, 17, 674-679
    • (2007) Curr. Opin. Struct. Biol. , vol.17 , pp. 674-679
    • Robertson, J.G.1
  • 15
    • 0036181649 scopus 로고    scopus 로고
    • Protein tyrosine phosphatases: Structure and function, substrate specificity, and inhibitor development
    • Zhang, Z. Y. Protein tyrosine phosphatases: Structure and function, substrate specificity, and inhibitor development Annu. Rev. Pharmacol. Toxicol. 2002, 42, 209-234
    • (2002) Annu. Rev. Pharmacol. Toxicol. , vol.42 , pp. 209-234
    • Zhang, Z.Y.1
  • 17
    • 33748263629 scopus 로고    scopus 로고
    • Pseudobond ab initio QM/MM approach and its applications to enzyme reactions
    • Zhang, Y. Pseudobond ab initio QM/MM approach and its applications to enzyme reactions Theor. Chem. Acc. 2006, 116, 43-50
    • (2006) Theor. Chem. Acc. , vol.116 , pp. 43-50
    • Zhang, Y.1
  • 18
    • 43949083733 scopus 로고    scopus 로고
    • Free Energies of Chemical Reactions in Solution and in Enzymes with Ab Initio Quantum Mechanics/Molecular Mechanics Methods
    • Hu, H.; Yang, W. T. Free Energies of Chemical Reactions in Solution and in Enzymes with Ab Initio Quantum Mechanics/Molecular Mechanics Methods Annu. Rev. Phys. Chem. 2008, 59, 573-601
    • (2008) Annu. Rev. Phys. Chem. , vol.59 , pp. 573-601
    • Hu, H.1    Yang, W.T.2
  • 19
    • 60349127442 scopus 로고    scopus 로고
    • QM/MM methods for biomolecular systems
    • Senn, H. M.; Thiel, W. QM/MM methods for biomolecular systems Angew. Chem., Int. Ed. 2009, 48, 1198-1229
    • (2009) Angew. Chem., Int. Ed. , vol.48 , pp. 1198-1229
    • Senn, H.M.1    Thiel, W.2
  • 20
    • 79959339177 scopus 로고    scopus 로고
    • Paradynamics: An Effective and Reliable Model for Ab lnitio QM/MM Free-Energy Calculations and Related Tasks
    • Plotnikov, N. V.; Kamerlin, S. C. L.; Warshel, A. Paradynamics: An Effective and Reliable Model for Ab lnitio QM/MM Free-Energy Calculations and Related Tasks J. Phys. Chem. B 2011, 115, 7950-7962
    • (2011) J. Phys. Chem. B , vol.115 , pp. 7950-7962
    • Plotnikov, N.V.1    Kamerlin, S.C.L.2    Warshel, A.3
  • 21
    • 48749103219 scopus 로고    scopus 로고
    • Extensive Conformational Transitions Are Required to Turn on ATP Hydrolysis in Myosin
    • Yang, Y.; Yu, H.; Cui, Q. Extensive Conformational Transitions Are Required to Turn On ATP Hydrolysis in Myosin J. Mol. Biol. 2008, 381, 1407-1420
    • (2008) J. Mol. Biol. , vol.381 , pp. 1407-1420
    • Yang, Y.1    Yu, H.2    Cui, Q.3
  • 22
    • 78651371352 scopus 로고    scopus 로고
    • 2+ Ion in the Reaction Coordinate of RNA Self-Cleavage Catalyzed by the Hammerhead Ribozyme
    • 2+ Ion in the Reaction Coordinate of RNA Self-Cleavage Catalyzed by the Hammerhead Ribozyme J. Chem. Theory Comput. 2011, 7, 1-3
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 1-3
    • Wong, K.Y.1    Lee, T.S.2    York, D.M.3
  • 23
    • 84855669291 scopus 로고    scopus 로고
    • QM/MM analysis suggests that Alkaline Phosphatase (AP) and Nucleotide pyrophosphatase/phosphodiesterase (NPP) slightly tighten the transition state for phosphate diester hydrolysis relative to solution: Implication for catalytic promiscuity in the AP superfamily
    • Hou, G. H.; Cui, Q. QM/MM analysis suggests that Alkaline Phosphatase (AP) and Nucleotide pyrophosphatase/phosphodiesterase (NPP) slightly tighten the transition state for phosphate diester hydrolysis relative to solution: implication for catalytic promiscuity in the AP superfamily J. Am. Chem. Soc. 2012, 134, 229-246
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 229-246
    • Hou, G.H.1    Cui, Q.2
  • 24
    • 84880385206 scopus 로고    scopus 로고
    • Stabilization of Different Types of Transition States in a Single Enzyme Active Site: QM/MM Analysis of Enzymes in the Alkaline Phosphatase Superfamily
    • Hou, G. H.; Cui, Q. Stabilization of Different Types of Transition States in a Single Enzyme Active Site: QM/MM Analysis of Enzymes in the Alkaline Phosphatase Superfamily J. Am. Chem. Soc. 2013, 135, 10457-10469
    • (2013) J. Am. Chem. Soc. , vol.135 , pp. 10457-10469
    • Hou, G.H.1    Cui, Q.2
  • 25
    • 84881084908 scopus 로고    scopus 로고
    • Modeling catalytic promiscuity in the alkaline phosphatase superfamily
    • Duarte, F.; Amrein, B. A.; Kamerlin, S. C. L. Modeling catalytic promiscuity in the alkaline phosphatase superfamily Phys. Chem. Chem. Phys. 2013, 15, 11160-11177
    • (2013) Phys. Chem. Chem. Phys. , vol.15 , pp. 11160-11177
    • Duarte, F.1    Amrein, B.A.2    Kamerlin, S.C.L.3
  • 26
    • 79956114412 scopus 로고    scopus 로고
    • An SCC-DFTB/MD Study of the Adsorption of Zwitterionic Glycine on a Geminal Hydroxylated Silica Surface in an Explicit Water Environment
    • Zhao, Y. L.; Köppen, S.; Frauenheim, T. An SCC-DFTB/MD Study of the Adsorption of Zwitterionic Glycine on a Geminal Hydroxylated Silica Surface in an Explicit Water Environment J. Phys. Chem. C 2011, 115, 9615-9621
    • (2011) J. Phys. Chem. C , vol.115 , pp. 9615-9621
    • Zhao, Y.L.1    Köppen, S.2    Frauenheim, T.3
  • 27
    • 84887850314 scopus 로고    scopus 로고
    • An Explicit Consideration of Desolvation is Critical to Binding Free Energy Calculations of Charged Molecules at Ionic Surfaces
    • in press.
    • Mori, T.; Hamers, R. J.; Pedersen, J. A.; Cui, Q. An Explicit Consideration of Desolvation is Critical to Binding Free Energy Calculations of Charged Molecules at Ionic Surfaces. J. Chem. Theory Comput. 2013, 9, in press.
    • (2013) J. Chem. Theory Comput. , vol.9
    • Mori, T.1    Hamers, R.J.2    Pedersen, J.A.3    Cui, Q.4
  • 28
  • 29
    • 0346850729 scopus 로고    scopus 로고
    • Towards a "next generation" neglect of diatomic differential overlap based semiempirical molecular orbital technique
    • Winget, P.; Selçuki, C.; Horn, A. H. C.; Martin, B.; Clark, T. Towards a "next generation" neglect of diatomic differential overlap based semiempirical molecular orbital technique Theor. Chem. Acc. 2003, 110, 254-266
    • (2003) Theor. Chem. Acc. , vol.110 , pp. 254-266
    • Winget, P.1    Selçuki, C.2    Horn, A.H.C.3    Martin, B.4    Clark, T.5
  • 30
    • 80052815998 scopus 로고    scopus 로고
    • Benchmarking semiempirical methods for thermochemistry, kinetics, and noncovalent interactions: OMx methods are almost as accurate and robust as DFT-GGA methods for organic molecules
    • Korth, M.; Thiel, W. Benchmarking semiempirical methods for thermochemistry, kinetics, and noncovalent interactions: OMx methods are almost as accurate and robust as DFT-GGA methods for organic molecules J. Chem. Theory Comput. 2011, 7, 2929-2936
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 2929-2936
    • Korth, M.1    Thiel, W.2
  • 31
    • 84857002725 scopus 로고    scopus 로고
    • Density-functional expansion methods: Grand challenges
    • Giese, T. J.; York, D. M. Density-functional expansion methods: Grand challenges Theor. Chem. Acc. 2012, 131, 1145
    • (2012) Theor. Chem. Acc. , vol.131 , pp. 1145
    • Giese, T.J.1    York, D.M.2
  • 32
    • 1542779956 scopus 로고    scopus 로고
    • Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties
    • Elstner, M.; Porezag, D.; Jungnickel, G.; Elsner, J.; Haugk, M.; Frauenheim, T.; Suhai, S.; Seifert, G. Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties Phys. Rev. B 1998, 58, 7260-7268
    • (1998) Phys. Rev. B , vol.58 , pp. 7260-7268
    • Elstner, M.1    Porezag, D.2    Jungnickel, G.3    Elsner, J.4    Haugk, M.5    Frauenheim, T.6    Suhai, S.7    Seifert, G.8
  • 33
    • 33748283200 scopus 로고    scopus 로고
    • The SCC-DFTB method and its application to biological systems
    • Elstner, M. The SCC-DFTB method and its application to biological systems Theor. Chem. Acc. 2006, 116, 316-325
    • (2006) Theor. Chem. Acc. , vol.116 , pp. 316-325
    • Elstner, M.1
  • 35
    • 0001257583 scopus 로고
    • Construction of tight-binding-like potentials on the basis of density-functional theory: Application to carbon
    • Porezag, D.; Frauenheim, T.; Köhler, T.; Seifert, G.; Kaschner, R. Construction of tight-binding-like potentials on the basis of density-functional theory: Application to carbon Phys. Rev. B 1995, 51, 12947-12957
    • (1995) Phys. Rev. B , vol.51 , pp. 12947-12957
    • Porezag, D.1    Frauenheim, T.2    Köhler, T.3    Seifert, G.4    Kaschner, R.5
  • 36
    • 18644365762 scopus 로고    scopus 로고
    • Validation of the density-functional based tight-binding approximation method for the calculation of reaction energies and other data
    • Krüger, T.; Elstner, M.; Schiffels, P.; Frauenheim, T. Validation of the density-functional based tight-binding approximation method for the calculation of reaction energies and other data J. Chem. Phys. 2005, 122, 114110
    • (2005) J. Chem. Phys. , vol.122 , pp. 114110
    • Krüger, T.1    Elstner, M.2    Schiffels, P.3    Frauenheim, T.4
  • 37
    • 34547428921 scopus 로고    scopus 로고
    • Looking at self-consistent-charge density functional tight binding from a semiempirical perspective
    • Otte, N.; Scholten, M.; Thiel, W. Looking at self-consistent-charge density functional tight binding from a semiempirical perspective J. Phys. Chem. A 2007, 111, 5751-5755
    • (2007) J. Phys. Chem. A , vol.111 , pp. 5751-5755
    • Otte, N.1    Scholten, M.2    Thiel, W.3
  • 38
    • 33846700979 scopus 로고    scopus 로고
    • Comparison of SCC-DFTB and NDDO-based semiempirical molecular orbital methods for organic molecules
    • Sattelmeyer, K. W.; Tirado-Rives, J.; Jorgensen, W. L. Comparison of SCC-DFTB and NDDO-based semiempirical molecular orbital methods for organic molecules J. Phys. Chem. A 2006, 110, 13551-13559
    • (2006) J. Phys. Chem. A , vol.110 , pp. 13551-13559
    • Sattelmeyer, K.W.1    Tirado-Rives, J.2    Jorgensen, W.L.3
  • 39
    • 0035978897 scopus 로고    scopus 로고
    • Application of an approximate density-functional method to sulfur containing compounds
    • Niehaus, T. A.; Elstner, M.; Frauenheim, T.; Suhai, S. Application of an approximate density-functional method to sulfur containing compounds J. Mol. Struct.: THEOCHEM 2001, 541, 185-194
    • (2001) J. Mol. Struct.: THEOCHEM , vol.541 , pp. 185-194
    • Niehaus, T.A.1    Elstner, M.2    Frauenheim, T.3    Suhai, S.4
  • 40
    • 0141566583 scopus 로고    scopus 로고
    • Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: Applications to structural and energetic analysis
    • Elstner, M.; Cui, Q.; Munih, P.; Kaxiras, E.; Frauenheim, T.; Karplus, M. Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: Applications to structural and energetic analysis J. Comput. Chem. 2003, 24, 565-581
    • (2003) J. Comput. Chem. , vol.24 , pp. 565-581
    • Elstner, M.1    Cui, Q.2    Munih, P.3    Kaxiras, E.4    Frauenheim, T.5    Karplus, M.6
  • 41
    • 65249089684 scopus 로고    scopus 로고
    • Toward an Accurate Density-Functional Tight-Binding Description of Zinc-Containing Compounds
    • Moreira, N. H.; Dolgonos, G.; Aradi, B.; da Rosa, A. L.; Frauenheim, T. Toward an Accurate Density-Functional Tight-Binding Description of Zinc-Containing Compounds J. Chem. Theory Comput. 2009, 5, 605-614
    • (2009) J. Chem. Theory Comput. , vol.5 , pp. 605-614
    • Moreira, N.H.1    Dolgonos, G.2    Aradi, B.3    Da Rosa, A.L.4    Frauenheim, T.5
  • 42
    • 84860839601 scopus 로고    scopus 로고
    • A Complete Set of Self-Consistent Charge Density-Functional Tight-Binding Parametrization of Zinc Chalcogenides (ZnX; X=O, S, Se, and Te)
    • Saha, S.; Pal, S.; Sarkar, P.; Rosa, A. L.; Frauenheim, T. A Complete Set of Self-Consistent Charge Density-Functional Tight-Binding Parametrization of Zinc Chalcogenides (ZnX; X=O, S, Se, and Te) J. Comput. Chem. 2012, 33, 1165-1178
    • (2012) J. Comput. Chem. , vol.33 , pp. 1165-1178
    • Saha, S.1    Pal, S.2    Sarkar, P.3    Rosa, A.L.4    Frauenheim, T.5
  • 43
    • 58149235077 scopus 로고    scopus 로고
    • Description of phosphate hydrolysis reactions with the Self-Consistent-charge Density-Functional-Tight-Binding (SCC-DFTB) theory. 1. Parameterization
    • Yang, Y.; Yu, H.; York, D.; Elstner, M.; Cui, Q. Description of phosphate hydrolysis reactions with the Self-Consistent-charge Density-Functional-Tight- Binding (SCC-DFTB) theory. 1. Parameterization J. Chem. Theory Comput. 2008, 4, 2067-2084
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 2067-2084
    • Yang, Y.1    Yu, H.2    York, D.3    Elstner, M.4    Cui, Q.5
  • 44
    • 34547451681 scopus 로고    scopus 로고
    • Application of the computationally efficient self-consistent-charge density-functional tight-binding method to magnesium-containing molecules
    • Cai, Z.; Lopez, P.; Reimers, J. R.; Cui, Q.; Elstner, M. Application of the computationally efficient self-consistent-charge density-functional tight-binding method to magnesium-containing molecules J. Phys. Chem. A 2007, 111, 5743-5750
    • (2007) J. Phys. Chem. A , vol.111 , pp. 5743-5750
    • Cai, Z.1    Lopez, P.2    Reimers, J.R.3    Cui, Q.4    Elstner, M.5
  • 46
    • 36049006141 scopus 로고    scopus 로고
    • Parameter calibration of transition-metal elements for the spin-polarized self-consistent-charge density-functional tight-binding (DFTB) method: Sc, Ti, Fe, Co, and Ni
    • Zheng, G. S.; Witek, H. A.; Bobadova-Parvanova, P.; Irle, S.; Musaev, D. G.; Prabhakar, R.; Morokuma, K. Parameter calibration of transition-metal elements for the spin-polarized self-consistent-charge density-functional tight-binding (DFTB) method: Sc, Ti, Fe, Co, and Ni J. Chem. Theory Comput. 2007, 3, 1349-1367
    • (2007) J. Chem. Theory Comput. , vol.3 , pp. 1349-1367
    • Zheng, G.S.1    Witek, H.A.2    Bobadova-Parvanova, P.3    Irle, S.4    Musaev, D.G.5    Prabhakar, R.6    Morokuma, K.7
  • 47
    • 77950183357 scopus 로고    scopus 로고
    • An Improved Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) Set of Parameters for Simulation of Bulk and Molecular Systems Involving Titanium
    • Dolgonos, G.; Aradi, B.; Moreira, N. H.; Frauenheim, T. An Improved Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) Set of Parameters for Simulation of Bulk and Molecular Systems Involving Titanium J. Chem. Theory Comput. 2010, 6, 266-278
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 266-278
    • Dolgonos, G.1    Aradi, B.2    Moreira, N.H.3    Frauenheim, T.4
  • 49
    • 34547437377 scopus 로고    scopus 로고
    • SCC-DFTB: What is the proper degree of self-consistency
    • Elstner, M. SCC-DFTB: What is the proper degree of self-consistency J. Phys. Chem. A 2007, 111, 5614-5621
    • (2007) J. Phys. Chem. A , vol.111 , pp. 5614-5621
    • Elstner, M.1
  • 50
    • 35948946987 scopus 로고    scopus 로고
    • 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
    • Yang, Y.; Yu, H.; York, D.; Cui, Q.; Elstner, M. 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, 111, 10861-10873
    • (2007) J. Phys. Chem. A , vol.111 , pp. 10861-10873
    • Yang, Y.1    Yu, H.2    York, D.3    Cui, Q.4    Elstner, M.5
  • 51
    • 79954547473 scopus 로고    scopus 로고
    • DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB)
    • Gaus, M.; Cui, Q.; Elstner, M. DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB) J. Chem. Theory Comput. 2011, 7, 931-948
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 931-948
    • Gaus, M.1    Cui, Q.2    Elstner, M.3
  • 52
    • 84872145856 scopus 로고    scopus 로고
    • Parametrization and Benchmark of DFTB3 for Organic Molecules
    • Gaus, M.; Goez, A.; Elstner, M. Parametrization and Benchmark of DFTB3 for Organic Molecules J. Chem. Theory Comput. 2013, 9, 338-354
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 338-354
    • Gaus, M.1    Goez, A.2    Elstner, M.3
  • 53
    • 0038762283 scopus 로고    scopus 로고
    • Extension of MNDO to d orbitals: Parameters and results for the second-row elements and for the zinc group
    • Thiel, W.; Voityuk, A. A. Extension of MNDO to d orbitals: Parameters and results for the second-row elements and for the zinc group J. Phys. Chem. 1996, 100, 616-626
    • (1996) J. Phys. Chem. , vol.100 , pp. 616-626
    • Thiel, W.1    Voityuk, A.A.2
  • 54
    • 0345042108 scopus 로고
    • Chemical bonding in hypervalent molecules - The dominance of ionic bonding and negative hyperconjugation over d-orbital participation
    • Reed, A. E.; Schleyer, P. v. R. Chemical bonding in hypervalent molecules-the dominance of ionic bonding and negative hyperconjugation over d-orbital participation J. Am. Chem. Soc. 1990, 112, 1434-1445
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 1434-1445
    • Reed, A.E.1    Schleyer V. P, R.2
  • 55
    • 0032569184 scopus 로고    scopus 로고
    • Chemical bonding in hypervalent molecules revised. Application of the Atoms in Molecules Theory to Y-3 X and Y-3 XZ (Y = H or CH3; X = N, P or As; Z = O or S) compounds
    • Dobado, J. A.; Martinez-Garcia, H.; Molina, J. M.; Sundberg, M. R. Chemical bonding in hypervalent molecules revised. Application of the Atoms in Molecules Theory to Y-3 X and Y-3 XZ (Y = H or CH3; X = N, P or As; Z = O or S) compounds J. Am. Chem. Soc. 1998, 120, 8461-8471
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 8461-8471
    • Dobado, J.A.1    Martinez-Garcia, H.2    Molina, J.M.3    Sundberg, M.R.4
  • 57
    • 30444451496 scopus 로고    scopus 로고
    • Extension of the PDDG/PM3 Semiempirical Molecular Orbital Method to Sulfur, Silicon, and Phosphorus
    • Tubert-Brohman, I.; Guimarães, C. R. W.; Jorgensen, W. L. Extension of the PDDG/PM3 Semiempirical Molecular Orbital Method to Sulfur, Silicon, and Phosphorus J. Chem. Theory Comput. 2005, 1, 817-823
    • (2005) J. Chem. Theory Comput. , vol.1 , pp. 817-823
    • Tubert-Brohman, I.1    Guimarães, C.R.W.2    Jorgensen, W.L.3
  • 58
    • 35448937584 scopus 로고    scopus 로고
    • Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements
    • Stewart, J. J. P. Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements J. Mol. Model. 2007, 13, 1173-1213
    • (2007) J. Mol. Model. , vol.13 , pp. 1173-1213
    • Stewart, J.J.P.1
  • 59
    • 4243943295 scopus 로고    scopus 로고
    • Generalized Gradient Approximation Made Simple
    • Perdew, J. P.; Burke, K.; Ernzerhof, M. Generalized Gradient Approximation Made Simple Phys. Rev. Lett. 1996, 77, 3865-3868
    • (1996) Phys. Rev. Lett. , vol.77 , pp. 3865-3868
    • Perdew, J.P.1    Burke, K.2    Ernzerhof, M.3
  • 60
    • 70350430420 scopus 로고    scopus 로고
    • Automatized parametrization of SCC-DFTB repulsive potentials: Application to hydrocarbons
    • Gaus, M.; Chou, C.-P.; Witek, H.; Elstner, M. Automatized parametrization of SCC-DFTB repulsive potentials: Application to hydrocarbons J. Phys. Chem. A 2009, 113, 11866-11881
    • (2009) J. Phys. Chem. A , vol.113 , pp. 11866-11881
    • Gaus, M.1    Chou, C.-P.2    Witek, H.3    Elstner, M.4
  • 61
    • 84890789306 scopus 로고    scopus 로고
    • Density Functional Tight Binding (DFTB): Application to organic an biological molecules
    • in press
    • Gaus, M.; Cui, Q.; Elstner, M. Density Functional Tight Binding (DFTB): Application to organic an biological molecules. WIREs Comput. Mol. Sci. 2013, in press
    • (2013) WIREs Comput. Mol. Sci.
    • Gaus, M.1    Cui, Q.2    Elstner, M.3
  • 62
    • 84856048751 scopus 로고    scopus 로고
    • Possible improvements to the self-consistent-charges density-functional tight-binding method within the second order
    • Bodrog, Z.; Aradi, B. Possible improvements to the self-consistent- charges density-functional tight-binding method within the second order Phys. Status Solidi B 2012, 249, 259-269
    • (2012) Phys. Status Solidi B , vol.249 , pp. 259-269
    • Bodrog, Z.1    Aradi, B.2
  • 63
    • 80051662197 scopus 로고    scopus 로고
    • Automated repulsive parametrization for the DFTB method
    • Bodrog, Z.; Aradi, B.; Frauenheim, T. Automated repulsive parametrization for the DFTB method J. Chem. Theory Comput. 2011, 7, 2654-2664
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 2654-2664
    • Bodrog, Z.1    Aradi, B.2    Frauenheim, T.3
  • 64
    • 34547403718 scopus 로고    scopus 로고
    • Treatment of collinear and noncollinear electron spin within an approximate density functional based method
    • Köhler, C.; Frauenheim, T.; Hourahine, B.; Seifert, G.; Sternberg, M. Treatment of collinear and noncollinear electron spin within an approximate density functional based method J. Phys. Chem. A 2007, 111, 5622-5629
    • (2007) J. Phys. Chem. A , vol.111 , pp. 5622-5629
    • Köhler, C.1    Frauenheim, T.2    Hourahine, B.3    Seifert, G.4    Sternberg, M.5
  • 65
    • 9644277032 scopus 로고    scopus 로고
    • Density functional based calculations for Fe-n (n < = 32)
    • Kohler, C.; Seifert, G.; Frauenheim, T. Density functional based calculations for Fe-n (n < = 32) Chem. Phys. 2005, 309, 23-31
    • (2005) Chem. Phys. , vol.309 , pp. 23-31
    • Kohler, C.1    Seifert, G.2    Frauenheim, T.3
  • 67
    • 0001213712 scopus 로고    scopus 로고
    • Assessment of Gaussian-3 and density functional theories for a larger experimental test set
    • Curtiss, L. A.; Raghavachari, K.; Redfern, P. C.; Pople, J. A. Assessment of Gaussian-3 and density functional theories for a larger experimental test set J. Chem. Phys. 2000, 112, 7374-7383
    • (2000) J. Chem. Phys. , vol.112 , pp. 7374-7383
    • Curtiss, L.A.1    Raghavachari, K.2    Redfern, P.C.3    Pople, J.A.4
  • 68
    • 26044479374 scopus 로고    scopus 로고
    • Assessment of Gaussian-3 and density-functional theories on the G3/05 test set of experimental energies
    • Curtiss, L. A.; Redfern, P. C.; Raghavachari, K. Assessment of Gaussian-3 and density-functional theories on the G3/05 test set of experimental energies J. Chem. Phys. 2005, 123, 124107
    • (2005) J. Chem. Phys. , vol.123 , pp. 124107
    • Curtiss, L.A.1    Redfern, P.C.2    Raghavachari, K.3
  • 69
    • 0013616075 scopus 로고
    • Direct dynamics calculations with NDDO (neglect of diatomic differential overlap) molecular orbital theory with specific reaction parameters
    • Gonzalez-Lafont, A.; Truong, T. N.; Truhlar, D. G. Direct dynamics calculations with NDDO (neglect of diatomic differential overlap) molecular orbital theory with specific reaction parameters J. Phys. Chem. 1991, 95, 4618-4627
    • (1991) J. Phys. Chem. , vol.95 , pp. 4618-4627
    • Gonzalez-Lafont, A.1    Truong, T.N.2    Truhlar, D.G.3
  • 71
    • 84898400240 scopus 로고    scopus 로고
    • DFTB - Density Functional based Tight Binding. (accessed on July 20th).
    • DFTB-Density Functional based Tight Binding. http://www.dftb.org (accessed on July 20th, 2012).
    • (2012)
  • 72
    • 84879999064 scopus 로고    scopus 로고
    • A Caveat on SCC-DFTB and Noncovalent Interactions Involving Sulfur Atoms
    • Petraglia, R.; Corminboeuf, C. A Caveat on SCC-DFTB and Noncovalent Interactions Involving Sulfur Atoms J. Chem. Theory Comput. 2013, 9, 3020-3025
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 3020-3025
    • Petraglia, R.1    Corminboeuf, C.2
  • 75
    • 0000109748 scopus 로고    scopus 로고
    • Assessment of Gaussian-2 and density functional theories for the computation of enthalpies of formation
    • Curtiss, L. A.; Raghavachari, K.; Redfern, P. C.; Pople, J. A. Assessment of Gaussian-2 and density functional theories for the computation of enthalpies of formation J. Chem. Phys. 1997, 106, 1063-1079
    • (1997) J. Chem. Phys. , vol.106 , pp. 1063-1079
    • Curtiss, L.A.1    Raghavachari, K.2    Redfern, P.C.3    Pople, J.A.4
  • 76
    • 46049088279 scopus 로고    scopus 로고
    • Performance of B3LYP density functional methods for a large set of organic molecules
    • Tirado-Rives, J.; Jorgensen, W. L. Performance of B3LYP density functional methods for a large set of organic molecules J. Chem. Theory Comput. 2008, 4, 297-306
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 297-306
    • Tirado-Rives, J.1    Jorgensen, W.L.2
  • 77
    • 35448937584 scopus 로고    scopus 로고
    • Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements
    • Stewart, J. J. P. Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements J. Mol. Model. 2007, 13, 1173-1213
    • (2007) J. Mol. Model. , vol.13 , pp. 1173-1213
    • Stewart, J.J.P.1
  • 78
    • 22444446541 scopus 로고    scopus 로고
    • Modeling vibrational spectra using the self-consistent charge density-functional tight-binding method II. Infrared spectra
    • Witek, H. A.; Morokuma, K.; Stradomska, A. Modeling vibrational spectra using the self-consistent charge density-functional tight-binding method II. Infrared spectra J. Chem. Theory Comput. 2005, 4, 639-655
    • (2005) J. Chem. Theory Comput. , vol.4 , pp. 639-655
    • Witek, H.A.1    Morokuma, K.2    Stradomska, A.3
  • 79
    • 23944526281 scopus 로고    scopus 로고
    • Accurate vibrational frequencies using the self-consistent-charge density-functional tight-binding method
    • Małolepsza, E.; Witek, H. A.; Morokuma, K. Accurate vibrational frequencies using the self-consistent-charge density-functional tight-binding method Chem. Phys. Lett. 2005, 412, 237-243
    • (2005) Chem. Phys. Lett. , vol.412 , pp. 237-243
    • Małolepsza, E.1    Witek, H.A.2    Morokuma, K.3
  • 80
    • 84857383281 scopus 로고    scopus 로고
    • Unique Stoichiometric Representation for Computational Thermochemistry
    • Fishtik, I. Unique Stoichiometric Representation for Computational Thermochemistry J. Phys. Chem. A 2012, 116, 1854-1863
    • (2012) J. Phys. Chem. A , vol.116 , pp. 1854-1863
    • Fishtik, I.1
  • 81
    • 24044444942 scopus 로고    scopus 로고
    • Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer
    • Range, K.; Riccardi, D.; Cui, Q.; Elstner, M.; York, D. M. Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer Phys. Chem. Chem. Phys. 2005, 7, 3070-3079
    • (2005) Phys. Chem. Chem. Phys. , vol.7 , pp. 3070-3079
    • Range, K.1    Riccardi, D.2    Cui, Q.3    Elstner, M.4    York, D.M.5
  • 82
    • 74649083341 scopus 로고    scopus 로고
    • Proton transfer function of carbonic anhydrase: Insights from QM/MM simulations
    • Riccardi, D.; Yang, S.; Cui, Q. Proton transfer function of carbonic anhydrase: Insights from QM/MM simulations Biochim. Biophys. Acta 2010, 1804, 342-351
    • (2010) Biochim. Biophys. Acta , vol.1804 , pp. 342-351
    • Riccardi, D.1    Yang, S.2    Cui, Q.3
  • 84
    • 79952943559 scopus 로고    scopus 로고
    • Effect of the damping function in dispersion corrected density functional theory
    • Grimme, S.; Ehrlich, S.; Goerigk, L. Effect of the damping function in dispersion corrected density functional theory J. Comput. Chem. 2011, 32, 1456-1465
    • (2011) J. Comput. Chem. , vol.32 , pp. 1456-1465
    • Grimme, S.1    Ehrlich, S.2    Goerigk, L.3
  • 85
    • 0035932162 scopus 로고    scopus 로고
    • Hydrogen bonding and stacking interactions of nucleic acid base pairs: A density functional-theory based treatment
    • Elstner, M.; Hobza, P.; Frauenheim, T.; Suhai, S.; Kaxiras, E. Hydrogen bonding and stacking interactions of nucleic acid base pairs: A density functional-theory based treatment J. Chem. Phys. 2001, 114, 5149-5155
    • (2001) J. Chem. Phys. , vol.114 , pp. 5149-5155
    • Elstner, M.1    Hobza, P.2    Frauenheim, T.3    Suhai, S.4    Kaxiras, E.5
  • 86
    • 70449348216 scopus 로고    scopus 로고
    • The hydrolysis activity of adenosine triphosphate in myosin: A theoretical analysis of anomeric effects and the nature of the transition state
    • Yang, Y.; Cui, Q. The hydrolysis activity of adenosine triphosphate in myosin: a theoretical analysis of anomeric effects and the nature of the transition state J. Phys. Chem. A 2009, 113, 12439-12446
    • (2009) J. Phys. Chem. A , vol.113 , pp. 12439-12446
    • Yang, Y.1    Cui, Q.2
  • 87
    • 65249093234 scopus 로고    scopus 로고
    • Does water relay play an important role in phosphoryl transfer reactions? Insights from theoretical study of a model reaction in water and tert-butanol
    • Yang, Y.; Cui, Q. Does water relay play an important role in phosphoryl transfer reactions? Insights from theoretical study of a model reaction in water and tert-butanol J. Phys. Chem. B 2009, 113, 4930-4939
    • (2009) J. Phys. Chem. B , vol.113 , pp. 4930-4939
    • Yang, Y.1    Cui, Q.2
  • 90
    • 33845926809 scopus 로고    scopus 로고
    • Improving the QM/MM description of chemical processes: A dual level strategy to explore the potential energy surface in very large systems
    • Marti, S.; Moliner, V.; Tuñón, I. Improving the QM/MM description of chemical processes: A dual level strategy to explore the potential energy surface in very large systems J. Chem. Theory Comput. 2005, 1, 1008-1016
    • (2005) J. Chem. Theory Comput. , vol.1 , pp. 1008-1016
    • Marti, S.1    Moliner, V.2    Tuñón, I.3
  • 92
    • 77955765435 scopus 로고    scopus 로고
    • Free energy calculations using dual-level Born-Oppenheimer molecular dynamics
    • Retegan, M.; Martins-Costa, M.; Ruiz-Lopez, M. F. Free energy calculations using dual-level Born-Oppenheimer molecular dynamics J. Chem. Phys. 2010, 133, 064103
    • (2010) J. Chem. Phys. , vol.133 , pp. 064103
    • Retegan, M.1    Martins-Costa, M.2    Ruiz-Lopez, M.F.3
  • 93
    • 84903362278 scopus 로고    scopus 로고
    • Quantum mechanics/molecular mechanics dual Hamiltonian free energy perturbation
    • Polyak, I.; Benighaus, T.; Boulanger, E.; Thiel, W. Quantum mechanics/molecular mechanics dual Hamiltonian free energy perturbation J. Chem. Phys. 2013, 139, 064105
    • (2013) J. Chem. Phys. , vol.139 , pp. 064105
    • Polyak, I.1    Benighaus, T.2    Boulanger, E.3    Thiel, W.4


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