Author
Thomas Hendrickson
Bio: Thomas Hendrickson is an academic researcher from Drexel University. The author has contributed to research in topics: Solvation & Solvent effects. The author has an hindex of 4, co-authored 4 publications receiving 7050 citations.
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TL;DR: An integrated molecular modeling system for designing and studying organic and bioorganic molecules and their molecular complexes using molecular mechanics is described in this article, which allows the construction, display and manipulation of molecules and complexes having as many as 10,000 atoms and provides interactive, state-of-the-art molecular mechanics on any subset of up to 1000 atoms.
Abstract: An integrated molecular modeling system for designing and studying organic and bioorganic molecules and their molecular complexes using molecular mechanics is described. The graphically controlled, atom-based system allows the construction, display and manipulation of molecules and complexes having as many as 10,000 atoms and provides interactive, state-of-the-art molecular mechanics on any subset of up to 1,000 atoms. The system semiautomates the graphical construction and analysis of complex structures ranging from polycyclic organic molecules to biopolymers to mixed molecular complexes. We have placed emphasis on providing effective searches of conformational space by a number of different methods and on highly optimized molecular mechanics energy calculations using widely used force fields which are supplied as external files. Little experience is required to operate the system effectively and even novices can use it to carry out sophisticated modeling operations. The software has been designed to run on Digital Equipment Corporation VAX computers interfaced to a variety of graphics devices ranging from inexpensive monochrome terminals to the sophisticated graphics displays of the Evans & Sutherland PS300 series.
3,507 citations
TL;DR: In this paper, it was shown that the active carbon incorporation catalyst is carbided iron and this conclusion was well supported by bulk carbon to iron stoichiometries of 0.1-0.25 estimated from the TPHT peak areas which were adequate to represent 40-60'36 conversion to bulk carbides such as Fe,C or FeSC2.
Abstract: sorption results9 revealed that the iron surface was mostly covered by promoter oxides of AI, Ca, and K. Postreaction XPS results also revealed a C( Is) XPS peak of weak to moderate intensity centered at 284.1-283.7 eV. This binding energy approaches those (ca. 283.5 eV) reported for iron cat bide^.^^*'^ More convincing evidence for carbide formation was obtained from TPHT results collected after reaction studies like those displayed in Figure 1 in which methane was the only product. After reaction at temperatures below 340 OC, only small amounts of reactive carbon could be distinguished with maximum methane desorption rates near 300 OC. However, for higher reaction temperatures, large amounts of methane were produced with a maximum rate just above 400 OC. Since XPS results revealed only small amounts of carbonaceous residue on top of the catalyst surface, this reactive carbon must be associated with carbiding of the catalyst. Consequently, it appears that the active carbon incorporation catalyst is carbided iron. This conclusion is well supported by bulk carbon to iron stoichiometries of 0.1-0.25 estimated from the TPHT peak areas which were adequate to represent 40-60'36 conversion to bulk carbides such as Fe,C or FeSC2. Moreover, preliminary results from studies using bona fide iron carbides have shown similar catalytic b e h a ~ i o r . ~
3,490 citations
189 citations
TL;DR: This study indicates that, in contrast to the single-copy pea seed lectin, the pea vegetative lectin is transcribed by at least four members of a highly conserved multigene family whose members are only distantly related to thepea seed Lectin at the primary amino-acid sequence level.
Abstract: We report the predicted sequence of four vegetative homologues (Blec1,2,3 and 4) of the pea seed lectin. This study indicates that, in contrast to the single-copy pea seed lectin (Kaminski et al., Plant Mol Biol 9: 497–507, 1987), the pea vegetative lectin is transcribed by at least four members of a highly conserved multigene family whose members are only distantly related to the pea seed lectin at the primary amino-acid sequence level. For example, Blec1 shares only 38% amino-acid identity with the pea seed lectin. However, molecular homology modelling predicts that Blec1 probably forms a similar tertiary structure to the pea seed lectin.
12 citations
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TL;DR: A general Amber force field for organic molecules is described, designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P, and halogens.
Abstract: We describe here a general Amber force field (GAFF) for organic molecules. GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P, and halogens. It uses a simple functional form and a limited number of atom types, but incorporates both empirical and heuristic models to estimate force constants and partial atomic charges. The performance of GAFF in test cases is encouraging. In test I, 74 crystallographic structures were compared to GAFF minimized structures, with a root-mean-square displacement of 0.26 A, which is comparable to that of the Tripos 5.2 force field (0.25 A) and better than those of MMFF 94 and CHARMm (0.47 and 0.44 A, respectively). In test II, gas phase minimizations were performed on 22 nucleic acid base pairs, and the minimized structures and intermolecular energies were compared to MP2/6-31G* results. The RMS of displacements and relative energies were 0.25 A and 1.2 kcal/mol, respectively. These data are comparable to results from Parm99/RESP (0.16 A and 1.18 kcal/mol, respectively), which were parameterized to these base pairs. Test III looked at the relative energies of 71 conformational pairs that were used in development of the Parm99 force field. The RMS error in relative energies (compared to experiment) is about 0.5 kcal/mol. GAFF can be applied to wide range of molecules in an automatic fashion, making it suitable for rational drug design and database searching.
13,615 citations
TL;DR: This paper presents a meta-modelling procedure called "Continuum Methods within MD and MC Simulations 3072", which automates the very labor-intensive and therefore time-heavy and expensive process of integrating discrete and continuous components into a discrete-time model.
Abstract: 6.2.2. Definition of Effective Properties 3064 6.3. Response Properties to Magnetic Fields 3066 6.3.1. Nuclear Shielding 3066 6.3.2. Indirect Spin−Spin Coupling 3067 6.3.3. EPR Parameters 3068 6.4. Properties of Chiral Systems 3069 6.4.1. Electronic Circular Dichroism (ECD) 3069 6.4.2. Optical Rotation (OR) 3069 6.4.3. VCD and VROA 3070 7. Continuum and Discrete Models 3071 7.1. Continuum Methods within MD and MC Simulations 3072
13,286 citations
TL;DR: The SMD model may be employed with other algorithms for solving the nonhomogeneous Poisson equation for continuum solvation calculations in which the solute is represented by its electron density in real space, including, for example, the conductor-like screening algorithm.
Abstract: We present a new continuum solvation model based on the quantum mechanical charge density of a solute molecule interacting with a continuum description of the solvent. The model is called SMD, where the “D” stands for “density” to denote that the full solute electron density is used without defining partial atomic charges. “Continuum” denotes that the solvent is not represented explicitly but rather as a dielectric medium with surface tension at the solute−solvent boundary. SMD is a universal solvation model, where “universal” denotes its applicability to any charged or uncharged solute in any solvent or liquid medium for which a few key descriptors are known (in particular, dielectric constant, refractive index, bulk surface tension, and acidity and basicity parameters). The model separates the observable solvation free energy into two main components. The first component is the bulk electrostatic contribution arising from a self-consistent reaction field treatment that involves the solution of the nonho...
10,945 citations
TL;DR: A new method, based on chemical thermodynamics, is developed for automatic detection of macromolecular assemblies in the Protein Data Bank (PDB) entries that are the results of X-ray diffraction experiments, as found, biological units may be recovered at 80-90% success rate, which makesX-ray crystallography an important source of experimental data on macromolescular complexes and protein-protein interactions.
8,377 citations
TL;DR: The development, current features, and some directions for future development of the Amber package of computer programs, which contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.
Abstract: We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.
7,672 citations