几种胡敏酸和富里酸分子结构模型的三维可视化与特性研究--《吉林农业大学》2007年硕士论文
几种胡敏酸和富里酸分子结构模型的三维可视化与特性研究
【摘要】：
选取几种经典的胡敏酸和富里酸模型，使其与金属离子和西玛嗪分子(有机农药分子)作用，将生成的结合物利用HyperChem软件绘制二维分子结构模型，然后将其进行三维转换和结构优化。据优化过程生成日志文件中的能量值、能量梯度及计算得出QSAR特征参数，从模型之间、模型与单体之间，对计算得到的三维模型性质加以对比和分析得出结论，通过主成分分析方法对上述结论进行验证。结果表明：
1从不同的HA与FA模型的疏水性顺序和O／C原子数比值排序对照可知，模拟腐殖酸模型的疏水性与该模型O／C原子数比值成反比，腐殖物质本身具有较强的亲水性(即较低的疏水性)，HA模型中的Dragunov—HA和FA模型中的Schnitzer和Khan模型更符合这一点。胡敏酸的Stevenson—HA、Dragunov—HA和富里酸的Alvarez-Puebla模型在水溶液中和高温条件下都能达到更好的稳定性。胡敏酸分子Dragunov—HA和富里酸分子Schnitzer和Khan模型比其它胡敏酸、富里酸分子模型的疏水性强，胡敏酸分子Felbeck—HA和富里酸分子Buffle—FA的折射性、极性比其它胡敏酸、富里酸分子模型强。
2在Hyperchem软件操作平台上，对几种胡敏酸、富里酸分子模型与金属离子K~+、Na~+、Cu~(2+)、Pb~(2+)的结合物进行三维模拟。从结合物模型之间、模型与单体之间对比结合物模型的QSAR参数，得出各种模型的特点。综合比较结果表明：Fuchs—HA和Alvarez—FA与金属离子结合物的疏水性小于其他它腐殖酸分子；Felbeck-HA和Buffle—FA与金属离子结合物的折射性、极性、近似表面积、栅格表面积、体积、质量同比小于其它腐殖酸分子。疏水性与折射性、极性、近似表面积、栅格表面、体积、质量在HA和FA与金属离子结合物模型上表现出的不同，应用主成分分析的结果正好验证了上述现象，说明此软件对于腐殖质结构设计具有一定的可信度。因此，我们得出Felbeck-HA和Buffle—FA与金属离子结合物相比其它模型结合物的结构更加合理。
3以Hyperchem软件为工具建立胡敏酸、富里酸与西玛嗪分子结合物模型，得出结论为：总的来说，与胡敏酸和富里酸单体相比，结合物的QSAR参数都增加了，其中Fuchs—HA和Alvarez—FA与西玛嗪分子结合物的疏水性、近似表面积同比小于其它结合物，然而，Felbeck-HA和Buffle—FA与西玛嗪分子结合物，在剩下的QSAR参数中，均同比小于结合物。主成分分析将疏水性和近似表面积划分为一组，其它的为另一组，这一分析结论恰好证明上面的性质。
【关键词】：
【学位授予单位】：吉林农业大学【学位级别】：硕士【学位授予年份】：2007【分类号】：Q50【目录】：
Abstract6-9
1. 前言9-16
1.1 Hyperchem软件与结构模型概述9-12
1.2 腐殖质与金属的作用12-14
1.3 腐殖质与有机污染物的相互作用14-15
1.4 本论文研究内容及目的15-16
2. 研究方法16-18
2.1 胡敏酸和富里酸单体二维分子结构模型的选取16
2.2 胡敏酸和富里酸三维分子结构模型图的绘制16-17
2.3 胡敏酸和富里酸三维分子结构模型的特性17-18
2.4 胡敏酸与富里酸分子模型的应用18
3. 结果与讨论18-68
3.1 胡敏酸和富里酸的三维分子结构模型及特性18-27
3.2 胡敏酸和富里酸分子与金属离子结合的三维模型及特性27-57
3.3 胡敏酸和富里酸分子与有机农药分子(除草剂)结合的三维模型及特性57-68
4. 结论68-70
参考文献70-74
作者简历75
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化学计算及分子结构
Open GL Rendering
The basic rendering modeling in HyperChem has been converted to a full new OpenGL model. This affects all the molecular rendering, giving a generally higher quality of graphics throughout the product.
Custom Color Support
It is now possible to color molecules, backgrounds, etc. using any of 16 million available colors rather than the traditional 8 standard colors that HyperChem has used in the past.
Mixed Renderings
The rendering of molecules supports different rendering for different parts of the same molecule. That is any atom can be rendered using any of the rendering molecules -- stick, balls, ball and stick, etc.
Tube Rendering of Atoms
A new &tube& rendering is now available for atoms.
Manipulate Protein Structures
Extensive additions have been made to HyperChem&s ability to deal with protein structures. HyperChem now supports four secondary structure descriptions - helices, sheets, turns, and coils. The secondary structures can be individual selected, colored, and rendered using a new secondary structure rendering capability.
Support for Secondary Structure Information in Protein Data Bank files
HyperChem recognizes and supports secondary structure information in its molecule files. Information from protein database (PDB) files is captured for and retained in HIN files. The peptide builder supports this new capability and adds a secondary structure description to all residues.
Protein Secondary Structure Rendering
Secondary structure rendering now includes ribbon lines, narrow ribbon sheets, thick ribbon sheets, encompassing helical cylinders and a coil rendering. These new renderings can be selected for any secondary structure or part of a secondary structure. They can be colored globally or colored differently for specific residues.
Enhanced Protein Builder Capability
In addition to alpha helices and beta sheets, the peptide builder now supports beta turns, parallel and anti-parallel beta sheets, left-handed alpha helices, 310-helices, and pi-helices.
Large Molecule Electron Density Approximation
A rapid new method is available for calculating and displaying the electron density and electrostatic potential of molecules. For example, the new method makes it practical to very quickly display the electron density of large proteins.
What is HyperChem?
HyperChem is a sophisticated molecular modeling environment that is known for its quality, flexibility, and ease of use. Uniting 3D visualization and animation with quantum chemical calculations, molecular mechanics, and dynamics, HyperChem puts more molecular modeling tools at your fingertips than any other Windows program.
Our newest version, HyperChem Release 7, is a full 32-bit application, developed for the Windows 95, 98, NT, ME, 2000 and XP operating systems. HyperChem Release 7 incorporates even more powerful computational chemistry tools than ever before, as well as newly incorporated modules, additional basis sets, new drawing capabilities and more.
What&s New in HyperChem Release 7?
Density Functional Package
Density Functional Theory (DFT) has been added as a basic computational engine to complement Molecular Mechanics, Semi-Empirical Quantum Mechanics and Ab Initio Quantum Mechanics. This new computational method comes with full capabilities including first and second derivatives so that all the capabilities of other earlier engines are also available with DFT. These include geometry optimization, infrared and optical spectra, molecular dynamics, Monte Carlo, etc.
A full complement of exchange and correlation functions is available, including eight exchange functionals and eight correlation functionals that can be combined in any fashion. Also included are four combination or hybrid functions, such as the popular B3-LYP or Becke-97 methods. A choice of various integration grids, controlling the method&s accuracy, is available to the user.
NMR Simulation
The HyperNMR package has been integrated into the core of HyperChem. This package allows for the simulation of NMR spectra. An accurante semi-empirical tailored specifically to NMR allows rapid interactive computation of NMR shielding constants (chemical shifts) and coupling constants for molecules as large as proteins. Basedon a solution of the quantum mechanical coupled-Hartree-Fock equations rather than simple database lookup, this package allows full exploration of NMR parameters in any situation, such as a new or novel chemical environment where simple database interpolation is impossible.
When appropriate, the NMR parameters can be integrated into a spin Hamiltonian to predict and display the full one-dimensional NMR spectra. The spectra can be manipulated to add line widths so as to simulate experimental spectra.
For more information on our NMR module, click here.
Database Package
A full database capability is integrated into HyperChem 7. This includes database search and retrieval of molecules for subsequent molecular modeling calculations as well as the storing of computed properties and optimized structures of your molecules in a new database. Included with the product is a sample database of 10,000 molecules that have previously been optimized with HyperChem. The sample database that is included is representative of common chemical compounds and can be used in a variety of ways associated with research in computational chemistry.
Database retrieval is simple and interactive and a variety of methods can be used to search a database, including a search for 2D or 3D structure. In conjunction with HyperChem&s scripting capability, a generic search based on appropriate computed properties is possible. That is, a question such as, &Give me all molecules whose stored or computed value of X is between x-d and x+d& is possible.
Charmm Protein Simulations
The Bio+ force field in HyperChem represents a version of the Chemistry at HARvard using Molecular Mechanics (Charmm) force field. Release 7 of HyperChem updates this force field with new functional terms and new parameters to represent the latest science from the Charmm community.
The new parameter sets for Charmm-19 represent new parameters for the bio+ force field of earlier versions of HyperChem, but parameter sets Charmm-22 and beyond represent a newer force field implemented in HyperChem 7 that includes a Urey-Bradley term describing interactions between the two terminal atoms of a 3-atom bond angle.
Typed Neglect of Differential Overlap (TNDO)
The Typed Neglect of Differential Overlap method is a new semi-empirical method that merges ideas from molecular mechanics and semi-empirical quantum mechanics. It is designed as a generic semi-empirical method capable of high accuracy when combined with the appropriate parameters. It uses the molecular mechanics idea of atom &typing& to describe the chemical environment of an atom in a molecule with different types being given different parameters. This is the key idea that gives molecular mechanics its validity and accuracy in the absence of any quantum mechanical capability. TNDO combines atom typing a basic quantum mechanical method and allows a rapid semi-empirical method to offer reliable results. The deficiency is the need to develop parameter sets for different types (different classes of molecules) as in molecular mechanics.
HyperChem 7 includes on a first step in this parameter generation but considerable research effort on the part of Hypercube, Inc., HyperChem users, and the general research community is needed to have parameter sets that cover a wide range of chemical situations. Hypercube&s web site will collect these parameter sets.
Molecules in Magnetic Fields
It is now possible to explore the structure and reactivity of molecular systems in a uniform magnetic field. HyperChem 6 added an optional external electric field to the workspace and HyperChem 7 adds an optional external magnetic field. The effect of magnetic fields is relatively unknown but this feature allows interactive exploration of how magnetic fields affect chemical behavior.
Two terms in the Hamiltonian are included. The first is the interaction of the magnetic field with the orbital angular momentum of electrons and the second is the Zeeman interaction of the magnetic field with the electrons& spin. This later term is only present with open-shell systems or calculations that use the Unrestricted Hartree-Fock calculations.
Optimization of the Geometry of Excited States
A new optimization method, Conjugate Directions, has been added. This method allows geometry optimization using only energies without the necessity of computing gradients (first derivatives). This opens up the possibility of optimizing structures for a number of new situations. In particular, any state of a Configuration Interaction calculation can be optimized. These include excited states for the first time.
Optimization of MP2 Correlated Geometries
A relatively accurate and relatively simple way of including electron correlation in ab initio calculations is Moller-Plesset second-order perturbation theory (MP2). Previously, HyperChem users could calculate MP2 energies only but now, using the Conjugate Directions optimizer mentioned above, they can calculate the optimized geometry of a structure using MP2 theory.
New Rendering of Aromatic Rings
While HyperChem is fundamentally a molecular modeling program, not a drawing program, it is convenient to have available the ability to easily create annotations of molecular structures and drawings that one can use in presentations. A principal deficiency in this regard has been the lack of a &pretty picture& of aromatic rings since HyperChem represents these with dotted lines, as is convenient for most situations where one is fundamentally interested in modeling not drawing. With HyperChem 7, it is now possible to represent aromatic rings as a more conventional ring with a circle in the middle of it, rather than a ring with dotted bonds.
Drawing Program
In the evolution of adding convenient drawing capabilities, as just mentioned, HyperChem 6 added the concept of annotations where text (essentially) could be add to the workspace to annotate chemical structures. These &text& annotations could include many symbols (such as arrows) using various fonts. With HyperChem 7 this drawing capability is extended to lines, ellipses (circles), and rectangles (squares). These elements can be colored, filled or unfilled, dotted, etc.
They are included in the latest HIN file standard so that HyperChem can be used as a simple drawing program.
Interactive Examination and Manipulation of Parameters
Molecular mechanics and semi-empirical methods use a large variety of parameters. In particular, the new TNDO method lends itself to a variety of parameter sets for a variety of different chemical computations. It has always been possible to edit the text-based parameter files and re-compile them. With HyperChem 7, it is possible to see parameters on-screen associated with selected atoms, bonds, torsions, etc. These can then be immediately edited if desired. In addition, it is possible, interactively, to copy whole parameter sets making it feasible to interactively explore different parameters sets in an easy fashion.
Enhanced Polymer Builder
The polymer builder has been enhanced to create branched polymers as well as linear polymers. As TAIL is attached to HEAD, it is possible to specify random attachment to either the new HEAD or an old HEAD, creating a branch in the polymer. In addition to explicitly specifying torsion angles for the HEAD to TAIL join, it is now possible to specify torsion angles for the internal bac specifically, one can have these monomer backbone angles chosen randomly or as originally specified in describing the monomer.
New Basis Sets
In conjunction with the new DFT capability of HyperChem 7, a large number of new basis sets have been added to the sets already included with HyperChem. These basis sets are available for either the ab initio module or the DFT module.
Feature Summary
Structure Input and Manipulation
Building molecules with HyperChem is simple: just choose an element from the periodic table, and click and drag with the mouse to sketch a structure. Mouse control of rotation around bonds, stereochemistry, and &rubber banding& of bonds makes changing structures easy. Extensive selection, highlighting, and display capabilities make it easy to focus on areas of interest in complex molecules.
Select, rotate, translate, and resize structures with convenient mouse controlled tools. Modify settings to control operation of tools.
Convert rough sketches into 3D structures with HyperChem&s model builder.
Apply builder constraints easily: specify bond lengths, bond angles, torsion angles, or the bonding geometry about a selected atom.
Specify atom type, atom charge, formal charge and atomic mass.
Build clusters and complex
move individual atoms and molecules as easily as you move groups.
Build peptides and nucleic acids from amino acid and nucleotide residue libraries.
Mutate residues and build large molecules incrementally (make changes at any point).
Add a periodic box of pre-equilibrated water molecules for aqueous solvation studies. Periodic boundary conditions can be used with other solvent systems, or without solvents.
Import structures from standard file formats: Brookhaven PDB, ChemDraw CHM, MOPAC Z-matrix, MDL MOL and ISIS Sketch, and Tripos MOL2 files.
Molecular Display
Display structures using ball and stick, fused CPK spheres, sticks, van der Waals dots, and sticks with vdW switch easily between rendering styles.
Specify shading and highlighting, stick width, and the radii of spheres. Stereo and perspective viewing are also available.
Display a Ray Traced image of the molecules in the workspace.
Select and name sets of atoms for custom display or monitoring of properties.
Set and display custom labels for atoms.
Display bond labels showing the current bond length or the currently computed quantum mechanical bond order.
Display protein backbones using ribbons, with optional display of sidechains.
Highlight potential hydrogen bond interactions.
Display dipole moment vectors and gradient vectors.
Computational Chemistry
Use HyperChem to explore quantum or classical model potential energy surfaces with single point, geometry optimization, or transition state search calculations. Include the effects of thermal motion with molecular dynamics, Langevin dynamics or Metropolis Monte Carlo simulations. User defined structural restraints may be added.
Types of Calculations
Single point calculations determine the molecular energy and properties for a given fixed geometry.
Geometry optimization calculations employ energy minimization algorithms to locate stable structures. Five minimization algorithms are provided.
Vibrational frequency calculations find the normal vibrational modes of an optimized structure. The vibrational spectrum can be displayed and the vibrational motions associated with specific transitions can be animated.
Transition state searching locates the metastable structures corresponding to transition states using either Eigenvector Following or Synchronous Transit methods. Molecular properties are then calculated.
Molecular dynamics simulations compute classical trajectories for molecular systems. Quantum forces can be used to model reactive collisions. Heating, equilibration, and cooling periods can be employed for simulated annealing and for studies of other temperature dependent processes. Both constant energy and constant temperature simulations are available.
Langevin dynamics simulations add frictional and stochastic forces to conventional molecular dynamics to model solvent collisional effects without inclusion of explicit solvent molecules.
Metropolis Monte Carlo simulations sample configurations from a statistical ensemble at a given temperature and are useful for exploring the possible configurations of a system as well as for computing temperature dependent equilibrium averages.
Computational Methods
Ab Initio Quantum Mechanics
Choose from many commonly used basis sets (STO-1G to D95**) including the standard STO-3G, 3-21G, 6-31G*, and 6-31G** basis sets
Extra basis functions ( s, p, d, sp, spd ) can be added to individual atoms or to groups of atoms.
Users can also define their own basis sets or modify existing basis sets easily using HyperChem&s documented basis set file format.
Semi-empirical Quantum Mechanics
HyperChem offers ten semi-empirical molecular orbital methods, with options for organic and main-group compounds, for transition metal complexes, and for spectral simulation.
Choose from Extended Huckel, CNDO, INDO, MINDO/3, MNDO, MNDO/d, AM1, PM3 (including transition metals), ZINDO/1 and ZINDO/S.
Molecular Mechanics
Four force fields provide computationally convenient methods for exploring the stability and dynamics of molecular systems.
Added flexibility of user defined atom types and parameters.
Choose from MM+, a general purpose force field, and three specialized biomolecule force fields: Amber, BIO+, and OPLS.
Mixed Mode Calculations
HyperChem allows you to perform quantum calculations on part of a molecular system, such as the solute, while treating the rest of the system classically. This boundary technique is available for all the quantum methods, with some limits for ab initio calculations.
Customize and Extend HyperChem with the Chemist&s Developer Kit
Streamline HyperChem&s menus. Add new graphical and co create custom menus for specific applications.
Interface to Visual Basic, C, C++ and FORTRAN programs. Add dialog boxes as well as menu items. For example, you could use HyperChem for visualization of structures and results from non-graphical quantum chemistry programs.
Link HyperChem procedures to other Windows programs such as MS Word and E direct selected results to these applications for convenient analysis and reporting.
Results with HyperChem
Rendering choices: Ball-and-stick, fused CPK spheres with optional shading and highlighting. Also vdW dots, cylinders and overlapping spheres.
Ribbon rendering for protein backbones, with optional sidechain display.
3D Isosurfaces or 2D contour plots of: total charge density, molecular orbitals, spin density, electrostatic potential (ESP), ESP mapped onto 3D charge density surface
Isosurface rendering choices: wire mesh, Jorgensen-Salem, transparent and solid surfaces, Gouraud shaded surface. User specified grid and isosurface value.
During simulations, display and average kinetic, potential, and total energy, as well as values of user specified bond lengths, bond angles, or torsion angles.
Animate vibrational modes.
Display2D or 3D potential energy plots
Customize and Automate
Construct custom menus
Automate routine operations with scripts
Send selected data to files or workspace
Add new features as menu items, or run from scripts
Interface and Extend
Construct a custom interface to programs written in VB, C/C++, or FORTRAN
Send HyperChem results to MS Word or Excel
Interface with other desktop programs
Relative stabilities of isomers
Heats of formation
Activation energies
Atomic charges
HOMO-LUMO energy gap
Ionization potentials
Electron affinities
Dipole moments
Electronic energy levels
MP2 electron correlation energy
CI excited state energy
Transition state structures and properties
Non-bonded interaction energy
UV-VIS absorption spectra
IR absorption spectra
Isotope effects on vibrations
Collision effects on structural properties
Stability of clusters
Save Results
Use Import/Export option to save results of quantum mechanics calculations or to view results generated by other programs.
Use HyperChem Data to store structures and properties in a custom molecular database.
Create Reaction Movies in AVI format.
Save as HTML page to store and display teh structure, orbitals, IR and UV spectra and IR spectra with normal modes.
Integrated Modules
The Raytrace module enables you to create stunning raytraced images of molecules in the workspace by bridging with the very high-level graphics visualization application known as Persistence of Vision (POV) Ray for Windows.
Automatically generate POV-Ray input files describing the molecule.
Run POV-Ray to generate high quality images in any of several graphic file formats supported by POV-Ray.
RMS Fit provides a new tool for comparing structures of molecules in HyperChem, augmenting the existing overlay function and the flexible fitting provided by restrained optimizations.
The RMS Fit module lets you carry out the following tasks:
Overlay two molecules by minimizing the distance between corresponding atoms in the two target molecules, displaying the residual error.
Have the corresponding atoms be all atoms, or selected atoms only.
Designate the corresponding atoms by their numbering within a molecule, or by the order in which you select them.
SEQUENCE EDITOR
Sequence Editor provides additional tools for manipulating strings of amino acids in HyperChem. The Sequence Editor brings the following capabilities to HyperChem:
Read FASTA files consisting of strings of one-letter amino acid designators.
Specify secondary structure, including alpha helix, extended, parallel and anti-parallel beta sheets, three types of beta turns, and random coil, and put the resulting structure into HyperChem.
Get polypeptides from HyperChem with secondary structure designators.
Search for specific amino acid sequences in a polypeptide.
Show the polarity of each amino acid in the sequence, and display the distribution of each type.
Compare the similarity of two polypeptides, using a Dayhoff matrix (dot plot) approach.
CRYSTAL BUILDER
With Crystal Builder you can build up crystals in HyperChem by hand, by entering fractional coordinates, or choose from a set of samples provided. Crystal Builder gives you control over the face you view, and the size of t it also allows you to read Cambridge Crystal Database files into HyperChem. The Crystal Builder includes the following features:
Read in Cambridge Crystallographic Database files (FDAT), and place them in HyperChem.
Over 20 sample crystal structures included, particularly useful in educational contexts.
Control crystal size and shape (number of unit cells in each direction).
Control which crystal face you view, by specifying Miller indices.
For manual building of crystals, you can specify unit cell angles and lengths (a, b, c) for each of the eight basic crystal types, plus face centered cubic and body-centered cubic. All distinct space groups are not included, so you may need to calculate special positions as required for the different space groups.
SUGAR BUILDER
With Sugar Builder you can construct polysaccharides from individual saccharide components. The Sugar Builder&s features include the following:
Build polysaccharides from aldoses and ketoses, as well as amino sugars and N-acyl sugars, Inositol and deoxy sugars.
Terminate the polysaccharides using any of the thirteen blocking groups provided.
For each saccharide, you have control over the isomer (D or L), the form (acyclic, a, or b), the angles (f, y and w), and the connection site.
Construct polymers from other, possibly non-saccharide, components using the user-defined component dialog box.
Link polysaccharide strands, with full specification of site and angles.
Carry out simulations, using an extension of the AMBER force field specifically intended for saccharides [S. W. Homans, Biochemistry 29, )]. This force field allows you to carry out calculations on some, but not all, polysaccharides. (HyperChem&s MM+ force field will also compute properties of polysaccharides).
CONFORMATIONAL SEARCH
The Conformational Search module is a tool for finding and saving stable structures of molecules, using stochastic approaches based on modification of torsion angles.
Conformational Search has a wide range of options to tune the search for your particular needs. The general approach is to twist selected torsion angles of the system to distort a structure and, if certain tests are met, optimize to obtain a new candidate structure. The new structure can be accepted or rejected as a structure of interest according to a variety of criteria. Here is a list of some of the more important facilities of Conformational Search:
Select the torsion angles you wish to vary using HyperChem&s selection methods.
Study ring flexibility using our implementation of the torsional flexing method of Kolossvary and Guida [J. Comput. Chem., 14, 691, (1993)].
Choose between random walk and a usage-directed approach [G. Chang, W. C. Guida and W. C. Still, J. Am. Chem. Soc., 111, )] to generate a sequence of conformations.
Save all acceptable structures as the run progresses, and restart previous searches.
Filter structures prior to optimization by checking for close contacts and torsion angles that are similar to previously optimized structures, and after optimization for inversion of chiral centers.
Following optimization, eliminate duplicate structures by comparing energies, torsion angles, and RMS fit residual errors, automatically taking account of user specified equivalent atoms.
Save full details of the search to a file. Structures can be read back in and put into HyperChem by simply selecting the structure of interest and executing a single command.
Display results in tables that can be copied into spreadsheets for further analysis.
QSAR PROPERTIES
QSAR Properties allows calculation and estimation of a variety of molecular descriptors commonly used in Quantitative Structure Activity Relationship (QSAR) studies. Most of the methods were developed for and are primarily applicable to organic molecules.
Here are some of the properties you can estimate using QSAR Properties:
Atomic charges, using the Gasteiger-Marsili method [Tetrahedron, 36, )].
Van der Waals and solvent accessible surface areas, using a rapid, approximate method due to W. C. Still and coworkers [W. Hasel, T. F. Hendrickson, W. C. Still, Tet. Comput. Meth., 1, 103 (1988)], or using a slower grid based method.
Molecular volumes, bounded by Van der Waals or solvent accessible surfaces, using a grid method.
Hydration energy (for peptides and similar systems), using our implementation of a method parametrized by Scheraga et al. [T. Ooi, M. Oobatake, G. Nemethy and H. Scheraga, Proc. Natl. Acad. Sci. USA 84, )], based on the approximate surface area calculation.
Log P (the log of the octanol-water partition coefficient), a hydrophobicity indicator, using our implementation of an atom fragment method developed by Ghose, Pritchett and Crippen [J. Comput. Chem., 9, 80 (1988)]. For a sample of organic molecules, the method yields a correlation coefficient (r) with experimental values of 0.92 and a standard error of 0.36.
Refractivity, also using an atom-based fragment method due to Ghose and Crippen [J. Chem. Inf. Comput. Sci., 27, 21 (1987)]. For a sample of organic molecules, the method yields a correlation coefficient (r) with experimental values of 0.995 and a standard error of 1.1.
Polarizability, using an atom-based method due to K. J. Miller [J. Am. Chem. Soc., 112, )]. For a sample of organic molecules, the method yields a correlation coefficient (r) with experimental values of 0.991 and a standard error of 9.3.
Mass, using a straightforward method.
QSAR Properties can compute the property for the current system in HyperChem, or operate in standalone mode with HyperChem Input (HIN) files.
Carry out batch calculations directly from spreadsheets supporting Windows Dynamic Data Exchange, using the spreadsheet macro language.
Send results to a results window, and save to&n,a log file.
SCRIPT EDITOR
HyperChem&s scripting capability is one of its most versatile features, allowing it to be controlled from outside using scripts or external programs. The Script Editor is a tool to assist you in developing scripts in the HyperChem language, and to send script messages directly to HyperChem as a command line.
Script Editor&s features include the following:
Send script messages directly to HyperChem using a command line.
Paste script messages from a dialog box, which lists all available script messages.
Read in your existing script files, and save lists of messages for later use.
Execute any number of script messages.
Retrieve information from HyperChem, display it in a window, and save it to a file. Results of calculations, or details of the current molecular system, can be saved in this manner.
New Force Fields
HyperChem added significant new capability to the AMBER method of molecular mechanics by including up-to-date modifications of this force field. AMBER code supports 5 parameter sets with their associated functional forms:
Amber for saccharides
Default Parameter Scheme for AMBER and OPLS
Any AMBER or OPLS computation can continue computing with default parameters, when explicit parameters are missing from the relevant parameter file. The normal AMBER and OPLS parameter scheme fails when explicit parameters associated with &atom types& are not available. with default parameters, no calculation fails for lack of parameters.
ESR Spectra
Calculated values of Hyperfine Coupling constants are also available, for characterizing the ESR spectra of open shell systems.
Electric Polarizabilities
Computation of polarizability tensors is available.
Plots of Potential Energy
You can select one or two structural features (bond length, torsion angle etc.) and request a plot of the potential energy as a function of either a single structural feature (2D plot) or two structural features (3D plot).
Protein Design
You can cut and paste any amino acid sequence. That is, a piece can be cut out, a piece inserted, or a sequence of one length replaced by a new sequence of a different length. Annealing operations are, of course, required for the rest of the protein to adapt to these modifications.
Electric Fields
It is possible to superimpose an applied electric field on any calculation. For example, a charged system will now drift in the workspace during a molecular dynamics run if an external electric field has been applied. Studying molecular behavior in an electric field is now possible.
Annotations
While it has always been possible to copy the rendering of molecules in HyperChem into a file or onto the clipboard and then transfer the rendering into a drawing or painting program to prepare overhead transparencies or other presentation material, directly creating such material without leaving HyperChem is now possible.
An annotation in HyperChem is a length of text that can be placed anywhere in the workspace. Because the text can have attributes such as a font, a color, and a size, it is possible to create annotations such as arrows, lines, circles, rectangles and any number of other drawing primitives. Annotating the molecules that are being modeled in HyperChem allows you to print the workspace and more easily describe to others the results of your modeling.
HyperChem contains a number of features associated with creating and manipulating these annotations. Because they exist in a plane or layer that is independent of the molecular or modeling plane, they augment rather than collide with the modeling of earlier versions of HyperChem. At the same time by being able to show or print both planes at the same time, a rich set of annotation options is possible.
While that is not the primary intent, HyperChem could now be used to prepare illustrations independent of chemistry and molecular modeling.
Charge and Multiplicity are Saved
The total charge and spin multiplicity are now stored in the HIN file and are restored when a molecular HIN file is read. Earlier, these had to be set interactively for any new molecule in the workspace.
Drawing Constraints
It is now possible to constrain your drawing of 2D molecules so that the the resultant drawn molecule has uniform bond lengths and angles and resembles a standard 2D molecular representation as might be seen in textbooks. These constraints have no effect on the subsequent 2D to 3D model building.
Graphical Display of Gradients
It is possible to visualize the gradient (force) on any atom as a vector. Any set of atoms can display these vectors.
Bond Labels
A set of dynamically updated labels are available for bonds as well as atoms and residues. These bond labels can be one of:
Bond length
Bond order - as calculated quantum mechanically
Enhanced Selection Capability
HyperChem operations depend to a great extent on one&s ability to select a subset of atoms. For example, it is possible to select atoms based on the range of various computed quantities such as their atomic charge or atomic gradient. Thus, for example, one can now select all atoms with a charge between -0.1 and 0.1.
The atom selection options are organized as either a selection based on a &string& property of an atom, such as the atom type (e.g. CH), or a &number& property such as the atom charge described above.
Whether you use HyperChem&s many internal features or build a live link with your other chemistry programs, the benefit of working with HyperChem Release 7 is that you are free to focus on the things that you do best. HyperChem does the rest.
For Further Information:
Molecular Mechanics with HyperChem
Quantum Mechanics with HyperChem
Visualization and Manipulation of Molecules with HyperChem
Structure Optimization with HyperChem
Extension and Customization with HyperChem
Molecular Dynamics with HyperChem
Molecular Mechanics with HyperChem
Molecular Mechanics
HyperChem software is a versatile tool for exploring the structure and stability of molecules. HyperChem integrates several molecular mechanics methods and an extensive suite of visualization and analysis tools to provide a powerful, easy-to-use, desktop molecular modeling program.
HyperChem provides simple ways to produce 3D molecular structures on screen, a choice of four force fields, geometry optimization techniques to search for stable structures, and molecular dynamics techniques to carry out conformational searching and to investigate structural changes.
Molecular Mechanics Applications
HyperChem&s molecular mechanics methods have many applications to the study of molecular structure and stability. Some typical applications are:
Calculating relative conformational energies of a series of analogous structures.
Re-optimizing a peptide after introducing a selective mutation.
Refining structures prior to more rigorous quantum mechanics calculations.
Assessing possible steric effects in a reactive intermediate.
To simulate the effects of solvent attenuation of electrostatic interactions, HyperChem offers a distance-dependent dielectric constant option for selected force fields.
Four Force Fields
HyperChem includes four built-in molecular mechanics force fields: new implementations of techniques developed and published by respected research groups.
Appropriate for most non-biological species.
Based on the MM2(1977) force field developed by N. L. Allinger.
Uses the 1991 parameter set.
Extended to incorporate nonbonded cutoffs, restraints, and periodic boundary conditions.
Computes default parameters for cases where MM2 parameters are not available.
Appropriate for use on polypeptides and nucleic acids with all hydrogen atoms explicitly included.
The AMBER force field was developed by the research group of P. A. Kollman.
Includes parameters for Versions 2.0 and 3.0a of this widely-used force field.
Designed for calculations on nucleic acids and peptides.
The OPLS united-atom force field was developed by the research group of W. L. Jorgensen.
The nonbonded interaction parameters are optimized for calculations where the solvent is explicitly included in the calculation.
Appropriate for use with HyperChem software&s built-in periodic water box.
Primarily designed to explore macromolecules.
Implements the CHARMM force field developed in the group of Martin Karplus.
Includes CHARMM parameters published for amino acids.
Allows users to add other parameter sets.
Adding Parameters
A recurring problem in working with molecular mechanics force fields is that of insufficient parameters. HyperChem tackles the problem by providing a default scheme for the MM+ force field and by allowing users to add their own parameters. All HyperChem force fields parameters are present as text files to which new atom types and new parameters can be easily added. The user can also define rules for automatic assignment of new atom types.
Quantum Mechanics with HyperChem
Quantum Mechanics
HyperChem software provides versatile tools for exploring the structure, stability and properties of molecules using quantum mechanics. There are simple ways to produce 3D molecular structures on screen. You choose from nine semi-empirical methods, and you can use geometry optimizers to search for stable structures or molecular dynamics techniques to model sample reaction trajectories. HyperChem allows you to easily add to or modify the semi-empirical quantum mechanics parameters in text files.
With HyperChem, you can perform semi-empirical calculations on elements hydrogen through xenon, including transition-metals. HyperChem includes a model builder that turns a rough 2D sketch of a molecule into 3D. HyperChem combines semi-empirical quantum mechanics and molecular mechanics methods in a single package to create a powerful tool for finding better starting geometries, substantially reducing computation time.
Quantum Mechanics Applications
HyperChem quantum mechanical methods have many practical applications to the study of molecular structure and properties, including:
Determining frontier orbital interactions between donor and acceptor molecules as illustrated by Diels-Alder cycloaddition reactions.
Obtaining partial atomic charges, using Mulliken population analysis, to predict likely sites of attack.
Generating electrostatic potential contour plots to illustrate likely trajectories of approach in drug-receptor docking.
Calculating unpaired spin densities to identify possible reactive sites on a molecule or for correlation with ESR data.
UV-Visible Spectroscopy
Predict wavelengths and intensities of electronic transitions.
Predict locations of non-spectroscopically active states.
IR Spectroscopy
Predict wave numbers and intensities of vibrational absorption lines.
Display motions of normal modes using vectors and animations.
Nine Semi-Empirical Methods
HyperChem includes nine semi-empirical quantum-mechanical methods that are implementations of methods developed and published by respected research groups. These methods range from the simple all-valence-electron method (Extended H&ckel) to among the most sophisticated and accurate semi-empirical methods currently available (AM1 and PM3).
The semi-empirical quantum mechanics methods available in HyperChem software are:
Extended H&ckel, developed by R. Hoffmann.
CNDO and INDO, developed by the research group lead by J. A. Pople.
MINDO/3, MNDO and AM1, developed by the research group of M. J. S. Dewar.
PM3, developed by J. J. P. Stewart.
ZINDO/1 and ZINDO/S developed by the research group led by M. Zerner.
Flexible and Powerful
Several options for electronic structure calculations are available:
Systems with any charge and with spin multiplicity up to four can be studied.
Restricted and Unrestricted Hartree-Fock (RHF/UHF)calculations on closed-shell and open-shell systems can be performed.
Ground states (for each spin multiplicity), and first excited singlet state can be calculated.
Configuration Interaction (CI) using orbital or energy criteria with singles only or microstate methods.
The number of atoms is limited only by the memory in your PC: calculations using over 200 atomic orbitals can be carried out on a PC with 4Mb of RAM.
You can obtain a variety of useful results with these calculations, including:
Contour plots of molecular orbitals, charge and spin densities, and electrostatic potential.
Displays of orbital energy-level diagrams.
A log file of numerical data, including energies, heats of formation (for NOO methods), dipole moments, molecular orbital coefficients, and the density matrix.
Plots and log file data that allow you to study chemical reactivity and heats of formation.
Visualization and Manipulation of Molecules with HyperChem
Building, Visualizing and Manipulating Molecules
HyperChem is an integrated desktop molecular modeling system. Its building, visualization and manipulation capabilities are linked to its extensive computational features. In addition to helping you better visualize 3D molecular structures, HyperChem lets you easily set up, perform and interpret results from a wide variety of simulations and computations, including geometry optimizations and molecular dynamics runs.
Building Molecules
HyperChem uses a simple sketch-and-build method for building molecules on the screen and offers several means of creating and modifying 3D molecular structures.
Model Builder
Converts a 2D sketch into a 3D structure.
Defines stereochemistry before or after model building.
Adds hydrogen atoms automatically.
Sets bond lengths and bond angles to appropriate values.
Uses sophisticated algorithms to set rings and cages to appropriate structures.
Tools for peptides and nucleic acids
Using HyperChem, you can easily select residues and specify secondary structures from a menu.
Tools for modifying molecules
Substitute an atom or change bond order with a mouse click.
Mutate amino acid or nucleotide residues.
Translate, rotate, reflect or invert all or part of a molecule.
Read and write files in HyperChem INput (HIN), Brookhaven Protein Databank (PDB), Isis Sketch (SKC), MDL (MOL), OPAC Z-matrix and Tripos (MOL2) formats.
Visualizing Structures
Molecules can be rendered on the screen in several modes: sticks (stereo optional), dot surfaces, disks, or space-filling shaded spheres. HyperChem includes an array of visualization and manipulation tools to help you better understand molecular structures. You can:
Highlight, color, or hide parts of a molecular system.
Display peptide structure using ribbons.
Color a DNA backbone one color throughout.
Color a substrate differently from an enzyme.
Highlight a particular ring in a complicated molecule.
Optionally display hydrogens.
View slices of molecules.
Display computational results.
Animate vibrational modes of molecules.
Consistency Gives Ease of Use
The HyperChem user interface consistently employs a select-and-operate method to simplify use. Simply select a set of atoms, residues or molecules with the mouse and then apply the desired operation or tool.
Making and naming selections
Selecting atoms, residues, or molecules is easy. You can select a particular ring, a specific side chain, a peptide or nucleic acid backbone, all atoms within a radius of a central atom, the shortest path between two atoms, or combine all these possibilities.
Once you have made a selection, you can &name& it for future use. Named selections are stored in HIN files and can be restored by picking the name from a menu.
Selections and Visualization
Selections can be used to control the display. You can:
Color a selection to distinguish it from the rest of a molecule.
Hide a selection from view, or hide the rest of the system, to focus on a region of particular interest.
Label a selection by element, type, chirality, residue name or charge.
Selections and Manipulations
You can apply an array of manipulation tools to selections to give complete control over molecule building. You can:
Rotate and translate a selected molecule or part of a molecule apart from the rest of the system.
Adjust selected bond lengths, bond angles and torsion angles.
Select a side chain in a molecule and rotate it about the connecting bond.
Invert and reflect selections, controlling stereochemistry and conformation.
Delete a selection, or copy and paste it using the clipboard.
Selections and Measurement
Selections provide a quick way to get at structural information. The atoms do not need to be bonded, so through-space measurements are easily made.
Selecting a single atom reports the type and position of that atom.
Selecting two atoms reports the distance between them.
Selecting three atoms reports the angle connecting them.
Selecting four atoms reports the dihedral angle.
Selections and Calculations
Selections enable restraints to be placed on molecular mechanics calculations, parts of molecules to be held frozen, and structural features to be tracked through dynamics runs.
Structure Optimization with HyperChem
Optimizing Molecular Structures
HyperChem combines optimization capabilities for quantum mechanics and molecular mechanics techniques with facilities for structure manipulation and visualization, molecular dynamics simulation and customization in an integrated, desk-top molecular-modeling system. With HyperChem, you can easily determine stable molecular structures. The added ability to handle restraints and selected parts of systems allows optimizers to become tools for investigation as well as refinement.
Straightforward Optimizing
Finding stable structures of molecules is probably the single most common computational task of molecular modeling programs. The relative energy of different optimized structures determines conformational stability, isomerization equilibria, heats of reaction, reaction products, and many other aspects of chemistry. HyperChem includes four optimizers:
A steepest descent optimizer, particularly useful for rapid removal of severe steric and strain problems in initial guess structures.
Two conjugate gradient optimizers (Fletcher-Reeves and Polak-Ribiere) for efficient convergence toward a minimum.
A block-diagonal Newton-Raphson optimizer (MM+ force field only), which moves one atom at a time using part of the second derivative information.
An Integrated Approach
HyperChem offers a truly integrated approach to structure optimization, providing efficiency, clarity and ease of use. This is feature of the overall design of the program provides several important benefits:
The same set of optimizers works with both molecular mechanics and semi-empirical quantum mechanics methods.
Optimization choices, such as termination conditions, frequency of screen update, and choice of algorithm, may be set in exactly the same way for all methods and all optimization algorithms.
The visual feedback on optimizations is provided in a consistent manner across methods.
The user retains full ability to rotate and translate the molecule while an optimization is in progress.
Selections
HyperChem makes extensive use of the ability to select a part of a system. Selections bring additional capabilities to the system in the context of optimizations.
Optimizing a Selection
If some atoms are selected when the optimization is started, only the selected atoms the rest of the system remains fixed.
HyperChem treats the unselected portion as a potential to be included in the quantum calculation. In this way, HyperChem allows the user to carry out quantum calculations on parts of a large system while still retaining the influence of the rest of that system.
Using selections for restraining forces
Selections enable you to build in restraining forces for distances, angles and dihedral angles between atoms that need not be bonded. Atoms can also be tethered to points in space. These restraints ha,,,,,,,,ve several applications:
To force a system towards a structure of interest.
To build structures from experimental data (such as distances or torsion angles deduced from NMR experiments).
Docking by Optimization
&Docking& a small molecule onto a site on a larger molecule is a common task in biochemical investigations. HyperChem&s extensive structure optimizing capabilities provide an effective route for exploring the structure of docked systems.
Given the two molecules, and a hypothesis as to which pairs of atoms are adjacent, the docking calculation can be started by constructing a set of optimizer restraints specifying those distances. Once these restraints are in place, select the small molecule, and optimize its structure. The restraint forces pull it into place in the docking site. Once complete, the restraints can be removed and a final optimization completed to get an accurate structure.
Docking is just one example of the kind of chemically interesting tasks that can be addressed using HyperChem optimization features.
Extension and Customization with HyperChem
HyperChem features two powerful tools that let you extend its functionality, build batch files, and customize the program: an extensive set of scripting commands, and the ability to communicate with other Windows programs via the Dynamic Data Exchange (DDE) standard protocol and the Windows Clipboard
Script Commands
A script command is a text instruction that tells HyperChem to carry out a task or requests information from HyperChem. A script is a text file containing a list of script commands, which are sent in sequence to HyperChem. The HyperChem documentation contains a full listing and description of more than 400 script commands.
Once a script file has been created, you can execute it from the HyperChem user interface, using the Script menu. Up to ten custom commands, complete with keyboard shortcuts, can appear on the Script menu. You can then simply click on a menu item to execute the appropriate script.
Scripts can be used in many ways to:
Carry out batch calculations.
Automate frequent tasks.
Set the visualization and computation options appropriate for different tasks.
Launch other programs from HyperChem.
Have HyperChem automatically read a particular file (called chem.scr) on startup to initialize your settings and carry out any task you always want executed upon start-up.
Ensure that a set of calculations is carried out with exactly the same settings in every case.
Dynamic Data Exchange and the Windows Clipboard
Windows programs can communicate by a well-defined protocol called Dynamic Data Exchange (DDE). HyperChem can also communicate using DDE, which means it can interact directly with other Windows applications. Among other things, DDE messages can send script commands to HyperChem from other applications. HyperChem can also exchange data with other Windows application through the Windows Clipboard, which allows you to copy images from HyperChem and paste them into other Windows programs.
Additionally, HyperChem provides a gateway to scientific databases such as the Brookhaven Protein Data Bank and to MDL Information Systems& ISIS database. Using the link between HyperChem and ISIS, you can build a 3D model from the data (with stereochemistry retained), perform calculations and modifications and then return the structure to the database.
HyperChem and Spreadsheets
You can write a macro in a Windows spreadsheet program that supports DDE (for example, Microsoft Excel) and bring spreadsheet capability to HyperChem. A macro can be used to:
Automatically carry out a set of calculations on a set of molecules and read the results into the spreadsheet for analysis and convenient organization of results.
Automatically carry out systematic searching of dihedral angles for stable conformations.
Carry out dynamics calculations and read the results into a spreadsheet for analysis.
HyperChem and Word Processors
Some word processors that run in Windows support DDE (for example, Microsoft Word). The combination of word processing tools and HyperChem visualization capabilities can greatly aid in the presentation of teaching and research materials. You can:
Place buttons in a document containing a lesson or tutorial that instruct HyperChem to carry out simulations illustrating the points you make in the text.
Cut and paste HyperChem images into documents.
Copy molecular dynamics plots into a Windows graphics programs to annotate them.
Paste numerical result into documents and update them automatically through dynamic data links as HyperChem produces new results.
Add-on Utilities and Programs for HyperChem
New intuitive and inexpensive software development tools, such as Microsoft Visual Basic, are rapidly reducing the work needed to create Windows programs. These tools help you construct programs that communicate with HyperChem and add to its functionality. The development of small utilities to carry out minor tasks as well as full-scale, add-on programs become much easier using these tools. The ChemPlus set of extensions for HyperChem are an example add-on programs that can greatly enhance the functionality of HyperChem.
Sharing HyperChem Add-ons
There is an electronic HyperChem discussion group on the Internet, so when you&ve built something that extends HyperChem capabilities, you can share it.
Molecular Dynamics with HyperChem
HyperChem provides versatile tools for exploring the structure, stability and properties of molecules using molecular mechanics and quantum mechanics. It offers simple ways to produce 3D molecular structures on screen, a choice of four molecular mechanics force fields and nine semi-empirical quantum mechanical methods, and a selection of geometry optimization techniques to search for stable structures. The graphical user interface links all of HyperChem&s extensive visualization and computational capabilities, giving you the ability to run molecular dynamics calculations using either molecular mechanics or quantum mechanics methods to calculate the interatomic forces.
Molecular Dynamics Applications
Molecular Dynamics calculations simulate the behavior of molecules at specified temperatures or energies and can be used in many applications, including:
Investigating conformational flexibility.
Using simulated annealing (high-temperature dynamics followed by slow cooling) to search for low-energy minima.
Using dynamics with restraining forces to build experimental data into your simulations.
Illustrating reaction mechanisms with dynamics trajectories using potential surfaces determined by semi-empirical quantum mechanical calculations.
Versatility in Molecular Dynamics Calculations
HyperChem offers a range of options for setting up molecular dynamics calculations, including the ability to:
Carry out molecular dynamics calculations using any of HyperChem&s molecular mechanics force fields or SCF quantum mechanical methods.
Run the calculations at constant energy, or keep the system close to a constant temperature.
Specify the length and temperature of the heating, run and cooling phases of a dynamics run.
Specify