Additional key references and background material on each of the modules are provided at appropri... more Additional key references and background material on each of the modules are provided at appropriate points throughout this manual.
We describe the work of the European project QUASI (Quantum Simulation in Industry, project EP250... more We describe the work of the European project QUASI (Quantum Simulation in Industry, project EP25047) which has sought to develop a flexible QM/MM scheme and to apply it to a range of industrial problems. A number of QM/MM approaches were implemented within the computational chemistry scripting system, ChemShell, which provides the framework for deploying a variety of independent program packages.
... 7b Only terminally bound halogens were considered. ... Details of the model geometries used a... more ... 7b Only terminally bound halogens were considered. ... Details of the model geometries used are provided in SUP 57619 ; (b) GAMESS-UK is a package of ab initio programs written by MF Guest, JH Van Lenthe, J. Kendrick, K. SchoffelP. ...
Low temperature crystal structures of (DABCO)H + Co(CO) 4 -(1) and (DABCO)H + Co-(CO) 3 PPh 3 -(2... more Low temperature crystal structures of (DABCO)H + Co(CO) 4 -(1) and (DABCO)H + Co-(CO) 3 PPh 3 -(2) (DABCO ) 1,4-diazabicyclooctane) indicate that both salts exhibit N-H‚‚‚ Co hydrogen bonding. IR and NMR data indicate that these hydrogen bonded species persist in nonpolar solvents such as toluene, but exist as solvent separated ions in more polar solvents. Replacement of the axial CO ligand by PPh 3 leads to a shortening of the N‚‚‚Co separation in the solid state from 3.437(3) to 3.294(6) Å. This change is accompanied by an increase in the angle between the equatorial carbonyl ligands. Thus, the crystallographic results suggest a strengthening of the N-H‚‚‚Co hydrogen bond upon increasing the basicity of the metal center, the first observation of this type in the solid state. This assertion is supported by variable-temperature 1 H and 13 C NMR data in toluene-d 8 solution which, discussed in the light of ab initio calculations, indicate that the barrier to a fluxional process involving cleavage of the N-H‚‚‚Co hydrogen bond is greater in 2 than in 1. The crystal structures of 1 and 2 have been determined by X-ray diffraction at 135(5) and 123(5) K, respectively [1 monoclinic, P2 1 /n (
Proceedings of The National Academy of Sciences, 2002
Evidence is emerging that mechanical stretching can alter the functional states of proteins. Fibr... more Evidence is emerging that mechanical stretching can alter the functional states of proteins. Fibronectin (Fn) is a large, extracellular matrix protein that is assembled by cells into elastic fibrils and subjected to contractile forces. Assembly into fibrils coincides with expression of biological recognition sites that are buried in Fn's soluble state. To investigate how supramolecular assembly of Fn into fibrillar matrix enables cells to mechanically regulate its structure, we used fluorescence resonance energy transfer (FRET) as an indicator of Fn conformation in the fibrillar matrix of NIH 3T3 fibroblasts. Fn was randomly labeled on amine residues with donor fluorophores and site-specifically labeled on cysteine residues in modules FnIII7 and FnIII15 with acceptor fluorophores. Intramolecular FRET was correlated with known structural changes of Fn in denaturing solution, then applied in cell culture as an indicator of Fn conformation within the matrix fibrils of NIH 3T3 fibroblasts.
Electronic differences between inorganic (M-X) and organic (C-X) halogens in conjunction with the... more Electronic differences between inorganic (M-X) and organic (C-X) halogens in conjunction with the anisotropic charge distribution associated with terminal halogens have been exploited in supramolecular synthesis based upon intermolecular M-X...X'-C halogen bonds. The synthesis and crystal structures of a family of compounds trans-[MCl(2)(NC(5)H(4)X-3)(2)] (M = Pd(II), Pt(II); X = F, Cl, Br, I; NC(5)H(4)X-3 = 3-halopyridine) are reported. With the exception of the fluoropyridine compounds, network structures propagated by M-Cl...X-C halogen bonds are adopted and involve all M-Cl and all C-X groups. M-Cl...X-C interactions show Cl...X separations shorter than van der Waals values, shorter distances being observed for heavier halogens (X). Geometries with near linear Cl...X-C angles (155-172 degrees ) and markedly bent M-Cl...X angles (92-137 degrees ) are consistently observed. DFT calculations on the model dimers {trans-[MCl(2)(NH(3))(NC(5)H(4)X-3)]}(2) show association through M-Cl...X-C (X not equal F) interactions with geometries similar to experimental values. DFT calculations of the electrostatic potential distributions for the compounds trans-[PdCl(2)(NC(5)H(4)X-3)(2)] (X = F, Cl, Br, I) demonstrate the effectiveness of the strategy to activate C-X groups toward halogen bond formation by enhancing their electrophilicity, and explain the absence of M-Cl...F-C interactions. The M-Cl...X-C halogen bonds described here can be viewed unambiguously as nucleophile-electrophile interactions that involve an attractive electrostatic contribution. This contrasts with some types of halogen-halogen interactions previously described and suggests that M-Cl...X-C halogen bonds could provide a valuable new synthon for supramolecular chemists.
... Understanding the Behavior of Halogens as Hydrogen Bond Acceptors. ... Halogens in each of th... more ... Understanding the Behavior of Halogens as Hydrogen Bond Acceptors. ... Halogens in each of these environments are found to engage in hydrogen bonding, and geometric preferences for these interactions have been established. ...
A second order Moller-Plesset (MP2) energy gradient algorithm for distributed memory parallel com... more A second order Moller-Plesset (MP2) energy gradient algorithm for distributed memory parallel computers is described. A direct approach is used in that integrals are recalculated as required, but the degree of recalculation is minimized by exploiting the large global memory typically available on parallel machines. Results, obtained using up to 256 processors of the Cray T3D show very good scalability,
A study of the equilibrium structures and relative energies for the conformers of 3-methylenepent... more A study of the equilibrium structures and relative energies for the conformers of 3-methylenepenta-1,4-diene (MPD) and bis(3,4-methylene)-1,5-hexadiene (MHD) have been obtained by SCF and MP2 correlated methods; a double zeta+polarisation basis set (DZP) was used. Both planar and non-planar forms were evaluated for a variety of point groups. The force constants for each conformer were obtained, in order to determine
In this paper, we review a series of hybrid QM/MM studies performed on the methanol synthesis cat... more In this paper, we review a series of hybrid QM/MM studies performed on the methanol synthesis catalyst. This work has required development of a new embedded cluster approach suitable for polar surfaces of ionic oxides, which has been implemented in the computer code ChemShell. Five themes have been pursued: simulation of polar oxide surfaces of ZnO; their hydrogenation; adsorption of reactants, intermediates and products on active sites; characterization of active sites by their spectroscopic signature; investigation of metal-support interactions and modeling of the formation and oxidation of supported nanoclusters.
We have investigated intrinsic point defects in ZnO and extended this study to Li, Cu and Al impu... more We have investigated intrinsic point defects in ZnO and extended this study to Li, Cu and Al impurity centres. Atomic and electronic structures as well as defect energies have been obtained for the main oxidation states of all defects using our embedded cluster hybrid quantum mechanical/molecular mechanical approach to the treatment of localised states in ionic solids. With these calculations we were able to explain the nature of a number of experimentally observed phenomena. We show that in zinc excess materials the energetics of zinc interstitial are very similar to those for oxygen vacancy formation. Our results also suggest assignments for a number of bands observed in photoluminescence and other spectroscopic studies of the material.
Grid computing is becoming an increasingly important way for computational scientists to access c... more Grid computing is becoming an increasingly important way for computational scientists to access computer resources. However, there is currently no consensus on the optimum middleware for providing access to these resources, or even a uniform way for users to interact with a particular middleware solution. As part of our work on the NW-GRID project, and in our development of our CCP1 GUI software, we have had cause to use two of these solutions (Globus and NorduGrid ARC), together with various client-side tools that are under development to support them. This paper describes our experiences to date with these different solutions, and work that has been carried out using some of them.
A description of the ab initio quantum chemistry package GAMESS-UK is presented. The package offe... more A description of the ab initio quantum chemistry package GAMESS-UK is presented. The package offers a wide range of quantum mechanical wavefunctions, capable of treating systems ranging from closed-shell molecules through to the species involved in complex reaction mechanisms. The availability of a wide variety of correlation methods provides the necessary functionality to tackle a number of chemically important tasks, ranging from geometry optimization and transition-state location to the treatment of solvation effects and the prediction of excited state spectra. With the availability of relativistic ECPs and the development of ZORA, such calculations may be performed on the entire Periodic including the lanthanides. Emphasis is given to the DFT module, which has been extensively developed in recent years, and a number of other, novel features of the program. The parallelization strategy used in the program is outlined, and detailed speedup results are given. Applications of the code in the areas of enzyme and zeolite catalysis and in spectroscopy are described.
For improvements to be made in long-standing industrial catalytic processes, an understanding of ... more For improvements to be made in long-standing industrial catalytic processes, an understanding of the atomistic mechanisms of the reactions occurring on the surface of the catalyst is required. A variety of experimental techniques can be used to derive information on sorption and reaction processes, but when both the catalyst and reactant mixtures are multicomponent, unambiguous identification of reaction mechanisms is difficult and often controversial. Computational techniques can, however, be used to gain valuable insight and interpret experimental evidence. Herein we show how new methods for modeling surface reactions on oxides can be used to elucidate key steps in a widely studied catalytic processthe conversion of CO 2 to methanol over oxide catalysts.
Additional key references and background material on each of the modules are provided at appropri... more Additional key references and background material on each of the modules are provided at appropriate points throughout this manual.
We describe the work of the European project QUASI (Quantum Simulation in Industry, project EP250... more We describe the work of the European project QUASI (Quantum Simulation in Industry, project EP25047) which has sought to develop a flexible QM/MM scheme and to apply it to a range of industrial problems. A number of QM/MM approaches were implemented within the computational chemistry scripting system, ChemShell, which provides the framework for deploying a variety of independent program packages.
... 7b Only terminally bound halogens were considered. ... Details of the model geometries used a... more ... 7b Only terminally bound halogens were considered. ... Details of the model geometries used are provided in SUP 57619 ; (b) GAMESS-UK is a package of ab initio programs written by MF Guest, JH Van Lenthe, J. Kendrick, K. SchoffelP. ...
Low temperature crystal structures of (DABCO)H + Co(CO) 4 -(1) and (DABCO)H + Co-(CO) 3 PPh 3 -(2... more Low temperature crystal structures of (DABCO)H + Co(CO) 4 -(1) and (DABCO)H + Co-(CO) 3 PPh 3 -(2) (DABCO ) 1,4-diazabicyclooctane) indicate that both salts exhibit N-H‚‚‚ Co hydrogen bonding. IR and NMR data indicate that these hydrogen bonded species persist in nonpolar solvents such as toluene, but exist as solvent separated ions in more polar solvents. Replacement of the axial CO ligand by PPh 3 leads to a shortening of the N‚‚‚Co separation in the solid state from 3.437(3) to 3.294(6) Å. This change is accompanied by an increase in the angle between the equatorial carbonyl ligands. Thus, the crystallographic results suggest a strengthening of the N-H‚‚‚Co hydrogen bond upon increasing the basicity of the metal center, the first observation of this type in the solid state. This assertion is supported by variable-temperature 1 H and 13 C NMR data in toluene-d 8 solution which, discussed in the light of ab initio calculations, indicate that the barrier to a fluxional process involving cleavage of the N-H‚‚‚Co hydrogen bond is greater in 2 than in 1. The crystal structures of 1 and 2 have been determined by X-ray diffraction at 135(5) and 123(5) K, respectively [1 monoclinic, P2 1 /n (
Proceedings of The National Academy of Sciences, 2002
Evidence is emerging that mechanical stretching can alter the functional states of proteins. Fibr... more Evidence is emerging that mechanical stretching can alter the functional states of proteins. Fibronectin (Fn) is a large, extracellular matrix protein that is assembled by cells into elastic fibrils and subjected to contractile forces. Assembly into fibrils coincides with expression of biological recognition sites that are buried in Fn's soluble state. To investigate how supramolecular assembly of Fn into fibrillar matrix enables cells to mechanically regulate its structure, we used fluorescence resonance energy transfer (FRET) as an indicator of Fn conformation in the fibrillar matrix of NIH 3T3 fibroblasts. Fn was randomly labeled on amine residues with donor fluorophores and site-specifically labeled on cysteine residues in modules FnIII7 and FnIII15 with acceptor fluorophores. Intramolecular FRET was correlated with known structural changes of Fn in denaturing solution, then applied in cell culture as an indicator of Fn conformation within the matrix fibrils of NIH 3T3 fibroblasts.
Electronic differences between inorganic (M-X) and organic (C-X) halogens in conjunction with the... more Electronic differences between inorganic (M-X) and organic (C-X) halogens in conjunction with the anisotropic charge distribution associated with terminal halogens have been exploited in supramolecular synthesis based upon intermolecular M-X...X'-C halogen bonds. The synthesis and crystal structures of a family of compounds trans-[MCl(2)(NC(5)H(4)X-3)(2)] (M = Pd(II), Pt(II); X = F, Cl, Br, I; NC(5)H(4)X-3 = 3-halopyridine) are reported. With the exception of the fluoropyridine compounds, network structures propagated by M-Cl...X-C halogen bonds are adopted and involve all M-Cl and all C-X groups. M-Cl...X-C interactions show Cl...X separations shorter than van der Waals values, shorter distances being observed for heavier halogens (X). Geometries with near linear Cl...X-C angles (155-172 degrees ) and markedly bent M-Cl...X angles (92-137 degrees ) are consistently observed. DFT calculations on the model dimers {trans-[MCl(2)(NH(3))(NC(5)H(4)X-3)]}(2) show association through M-Cl...X-C (X not equal F) interactions with geometries similar to experimental values. DFT calculations of the electrostatic potential distributions for the compounds trans-[PdCl(2)(NC(5)H(4)X-3)(2)] (X = F, Cl, Br, I) demonstrate the effectiveness of the strategy to activate C-X groups toward halogen bond formation by enhancing their electrophilicity, and explain the absence of M-Cl...F-C interactions. The M-Cl...X-C halogen bonds described here can be viewed unambiguously as nucleophile-electrophile interactions that involve an attractive electrostatic contribution. This contrasts with some types of halogen-halogen interactions previously described and suggests that M-Cl...X-C halogen bonds could provide a valuable new synthon for supramolecular chemists.
... Understanding the Behavior of Halogens as Hydrogen Bond Acceptors. ... Halogens in each of th... more ... Understanding the Behavior of Halogens as Hydrogen Bond Acceptors. ... Halogens in each of these environments are found to engage in hydrogen bonding, and geometric preferences for these interactions have been established. ...
A second order Moller-Plesset (MP2) energy gradient algorithm for distributed memory parallel com... more A second order Moller-Plesset (MP2) energy gradient algorithm for distributed memory parallel computers is described. A direct approach is used in that integrals are recalculated as required, but the degree of recalculation is minimized by exploiting the large global memory typically available on parallel machines. Results, obtained using up to 256 processors of the Cray T3D show very good scalability,
A study of the equilibrium structures and relative energies for the conformers of 3-methylenepent... more A study of the equilibrium structures and relative energies for the conformers of 3-methylenepenta-1,4-diene (MPD) and bis(3,4-methylene)-1,5-hexadiene (MHD) have been obtained by SCF and MP2 correlated methods; a double zeta+polarisation basis set (DZP) was used. Both planar and non-planar forms were evaluated for a variety of point groups. The force constants for each conformer were obtained, in order to determine
In this paper, we review a series of hybrid QM/MM studies performed on the methanol synthesis cat... more In this paper, we review a series of hybrid QM/MM studies performed on the methanol synthesis catalyst. This work has required development of a new embedded cluster approach suitable for polar surfaces of ionic oxides, which has been implemented in the computer code ChemShell. Five themes have been pursued: simulation of polar oxide surfaces of ZnO; their hydrogenation; adsorption of reactants, intermediates and products on active sites; characterization of active sites by their spectroscopic signature; investigation of metal-support interactions and modeling of the formation and oxidation of supported nanoclusters.
We have investigated intrinsic point defects in ZnO and extended this study to Li, Cu and Al impu... more We have investigated intrinsic point defects in ZnO and extended this study to Li, Cu and Al impurity centres. Atomic and electronic structures as well as defect energies have been obtained for the main oxidation states of all defects using our embedded cluster hybrid quantum mechanical/molecular mechanical approach to the treatment of localised states in ionic solids. With these calculations we were able to explain the nature of a number of experimentally observed phenomena. We show that in zinc excess materials the energetics of zinc interstitial are very similar to those for oxygen vacancy formation. Our results also suggest assignments for a number of bands observed in photoluminescence and other spectroscopic studies of the material.
Grid computing is becoming an increasingly important way for computational scientists to access c... more Grid computing is becoming an increasingly important way for computational scientists to access computer resources. However, there is currently no consensus on the optimum middleware for providing access to these resources, or even a uniform way for users to interact with a particular middleware solution. As part of our work on the NW-GRID project, and in our development of our CCP1 GUI software, we have had cause to use two of these solutions (Globus and NorduGrid ARC), together with various client-side tools that are under development to support them. This paper describes our experiences to date with these different solutions, and work that has been carried out using some of them.
A description of the ab initio quantum chemistry package GAMESS-UK is presented. The package offe... more A description of the ab initio quantum chemistry package GAMESS-UK is presented. The package offers a wide range of quantum mechanical wavefunctions, capable of treating systems ranging from closed-shell molecules through to the species involved in complex reaction mechanisms. The availability of a wide variety of correlation methods provides the necessary functionality to tackle a number of chemically important tasks, ranging from geometry optimization and transition-state location to the treatment of solvation effects and the prediction of excited state spectra. With the availability of relativistic ECPs and the development of ZORA, such calculations may be performed on the entire Periodic including the lanthanides. Emphasis is given to the DFT module, which has been extensively developed in recent years, and a number of other, novel features of the program. The parallelization strategy used in the program is outlined, and detailed speedup results are given. Applications of the code in the areas of enzyme and zeolite catalysis and in spectroscopy are described.
For improvements to be made in long-standing industrial catalytic processes, an understanding of ... more For improvements to be made in long-standing industrial catalytic processes, an understanding of the atomistic mechanisms of the reactions occurring on the surface of the catalyst is required. A variety of experimental techniques can be used to derive information on sorption and reaction processes, but when both the catalyst and reactant mixtures are multicomponent, unambiguous identification of reaction mechanisms is difficult and often controversial. Computational techniques can, however, be used to gain valuable insight and interpret experimental evidence. Herein we show how new methods for modeling surface reactions on oxides can be used to elucidate key steps in a widely studied catalytic processthe conversion of CO 2 to methanol over oxide catalysts.
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Papers by Paul Sherwood