Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme
TL;DR: Electrostatic stabilization is an important factor in increasing the rate of the reaction step that leads to the formation of the carbonium ion intermediate, found in the cleavage of a glycosidic bond by lysozyme.
About: This article is published in Journal of Molecular Biology.The article was published on 1976-05-15. It has received 3951 citations till now. The article focuses on the topics: Carbonium ion & Reaction step.
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TL;DR: The CHARMM (Chemistry at Harvard Macromolecular Mechanics) as discussed by the authors is a computer program that uses empirical energy functions to model macromolescular systems, and it can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations.
Abstract: CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a highly flexible computer program which uses empirical energy functions to model macromolecular systems. The program can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations. The operations that CHARMM can perform are described, and some implementation details are given. A set of parameters for the empirical energy function and a sample run are included.
14,725 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 software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s is described, which is a very fast program for molecular dynamics simulation.
Abstract: This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.
13,116 citations
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TL;DR: The “Activation‐strain TS interaction” (ATS) model of chemical reactivity is reviewed as a conceptual framework for understanding how activation barriers of various types of reaction mechanisms arise and how they may be controlled, for example, in organic chemistry or homogeneous catalysis.
Abstract: We present the theoretical and technical foundations of the Amsterdam Density Functional (ADF) program with a survey of the characteristics of the code (numerical integration, density fitting for the Coulomb potential, and STO basis functions). Recent developments enhance the efficiency of ADF (e.g., parallelization, near order-N scaling, QM/MM) and its functionality (e.g., NMR chemical shifts, COSMO solvent effects, ZORA relativistic method, excitation energies, frequency-dependent (hyper)polarizabilities, atomic VDD charges). In the Applications section we discuss the physical model of the electronic structure and the chemical bond, i.e., the Kohn–Sham molecular orbital (MO) theory, and illustrate the power of the Kohn–Sham MO model in conjunction with the ADF-typical fragment approach to quantitatively understand and predict chemical phenomena. We review the “Activation-strain TS interaction” (ATS) model of chemical reactivity as a conceptual framework for understanding how activation barriers of various types of (competing) reaction mechanisms arise and how they may be controlled, for example, in organic chemistry or homogeneous catalysis. Finally, we include a brief discussion of exemplary applications in the field of biochemistry (structure and bonding of DNA) and of time-dependent density functional theory (TDDFT) to indicate how this development further reinforces the ADF tools for the analysis of chemical phenomena. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 931–967, 2001
8,490 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
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TL;DR: In this paper, an extension of the Onsager theory of dielectric polarization is presented, which is applied to liquid water under the assumption of tetrahedral coordination and directed bonds between neighboring molecules.
Abstract: An extension of the Onsager theory of dielectric polarization is presented. The local dielectric constant is approximated by the macroscopic dielectric constant of the fluid in a region outside a molecule and its first shell of neighbors rather than in the entire region exterior to the molecule. In addition to the molecular dipole moment, the average value 〈cosγ〉Av of the cosine of the angle between neighbor dipoles is a determining factor. Hindered relative rotation of neighboring molecules produces a correlation between their orientations and prevents 〈cosγ〉Av from vanishing. The theory is applied to liquid water under the assumption of tetrahedral coordination and directed bonds between neighboring molecules.
1,660 citations
TL;DR: Polarization of the system due to the buried negative charge of the aspartic acid residue would make the serine oxygen strongly nucleophilic and would explain its reactivity towards amides and esters.
Abstract: The catalytic site of chymotrypsin contains an interior aspartic acid hydrogen-bonded to a histidine which in its turn is hydrogen-bonded to a serine. Polarization of the system due to the buried negative charge of the aspartic acid residue would make the serine oxygen strongly nucleophilic and would explain its reactivity towards amides and esters.
967 citations
TL;DR: In this article, Levitt and Levitt developed a method for the consistent calculation of ground and excited state potential surfaces of conjugated molecules, which is based on the formal separation of u and 7r electrons, the former being represented by an empirical potential function and the latter by a semi-empirical model of the Pariser-Parr-Pople type corrected for nearest-neighbor orbital overlap.
Abstract: A formulation is developed for the consistent calculation of ground and excited state potential surfaces of conjugated molecules. The method is based on the formal separation of u and 7r electrons, the former being represented by an empirical potential function and the latter by a semiempirical model of the Pariser-Parr-Pople type corrected for nearest-neighbor orbital overlap. A single parameter set is used to represent all of the molecular properties considered; these include atomization energies, electronic excitation energies, ionization potentials, and the equilibrium geometries and vibrational frequencies of the ground and excited electronic states, and take account of all bond length and bond angle variations. To permit rapid determination of the potential surfaces, the u potential function and SCF-MO-CI energy of the r electrons are expressed as analytic functions of the molecular coordinates from which the first and second derivatives can be obtained. Illustrative applications to 1,3butadiene, 1,3,5-hexatriene, a,w-diphenyloctatetraene, and 1,3-cyclohexadiene are given. detailed interpretation of electronic transitions and A concomitant photochemical processes in conjugated molecules requires a knowledge of the ground and excited state potential surfaces. The determination of such surfaces has long been a goal of theoretical chemistry. Difficulties in a reliable a priori approach to the problem for a system as simple as ethylene2 are such that calculations for more complicated molecules are prohibitive at present. Consequently, a variety of methods that utilize experimental data have been introduced. Completely empirical treatments, in which the energy surface is expressed as a function of potential parameters fitted to the available information (1) Supported in part by Grant EY00062 from the National Institute of Health. (2) U. Kaldor and I. Shavitt, J . Chem. Phys., 48, 191 (1968); R. J. Buenker, S. D. Peyerimhoff, and W. E. Kammer, ibid., 55, 814 (1971). (equilibrium geometry, vibrational frequencies, etc.), have had considerable success in applications to molecules for which a localized electron description is app l i~ab le .~ The great advantage of this type of approach, which leaves open questions of reliability when extended from one class of molecules to another, is the ease and speed of the calculations; this had made possible applications to systems as large as certain nucleic acids and globular proteins. For conjugated molecules, however, the importance of delocalization introduces difficulties into such an empirical treatmenL5 (3) (a) See, for example, J. E. Williams, P. J . Stand, and P. v. R. Schleyer, Annu. Reu. Phys. Chem., 19, 531 (1969); (b) S. Lifson and A. Warshel, J . Chem. Phys., 49, 5116 (1968); A. Warshel and S . Lifson, ibid., 53, 8582 (1970). (4) M. Levitt and S. Lifson, J. Mol. B i d , 46, 269 (1969); M. Levitt, Nature (London), 224, 759 (1969). ( 5 ) C. Tric, J . Chem. Phys., 5 1 , 4778 (1969). Journal of the American Chemical Society 1 94:16 1 August 9, 1972
676 citations