HyperChem V 8.0

張貼者:2010年9月18日 下午11:38未知的使用者   [ eddie liu 已於 2011年5月10日 下午7:54 更新 ]
HyperChem的 是一個複雜的分子模擬環境,以其高質量,靈活性和易用性。三維可視化和動畫團結與量子化學計算,分子力學,動力學, HyperChem的分子建模工具使更多的在你的指尖比其他任何Windows程序。 






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開發商:Hypercube Inc.
原廠網址:http://www.hyper.com/Products/HyperChemProfessional/ProFeatures/tabid/362/Default.aspx
更新日期:2011/05/11
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HyperChem特點

 
 
   
 
 
  
 
 

結構輸入和操作

建築用HyperChem的分子很簡單:只要選擇一個元素從元素週期表,點擊並拖動鼠標來素描的結構。 鼠標左右鍵控制的旋轉,立體,和“橡膠帶”的債券,使結構容易改變。 廣泛的選擇,突出和顯示功能可以很容易地專注於感興趣的領域中複雜的分子。

  • 選擇,旋轉,轉換,結構調整和便捷的鼠標控制的工具。 修改設置來控制操作的工具。
  • 粗略草圖轉換成三維結構與 HyperChem的'S模式的建設者。
  • 替換任何選定的氫與各種不同的取代基包括您自己的自定義取代。
  • 應用生成器的限制很容易:指定的鍵長,鍵角,扭轉角度,或結合幾何關於選定原子。
  • 指定類型的原子,原子電荷,正式起訴和原子的質量。
  • 建立集群和複雜的分子組裝;移動單個原子和分子一樣容易移動組。 
  • 構建多肽和核酸的氨基酸和核苷酸殘庫。
  • 發生突變殘基和逐步建立大型分子(在任何時候進行修改)。
  • 添加一個週期中前中平衡水分子的水得救的研究。 週期邊界條件可與其他溶劑系統,或者沒有溶劑。
  • 從進口結構標準的文件格式:布魯克海文臨時區議會,這適用於中藥,莫帕克的Z -矩陣,MDL公司商船三井和ISIS素描和榮譽學位 MOL2文件。

分子顯示

  • 顯示結構,堅持用球,電熔 CPK的領域,棒,球,圓柱,或管
  • 范德華點添加任何渲染。
  • 使用任何渲染任何原子在同一個分子。 
  • 指定棒或筒寬度和半徑的領域。
  • 立體聲和角度觀看,可同時作為質量設置。
  • 顯示一個光線跟踪的形象,分子在工作區。
  • 選擇和名稱設置為自定義顯示的原子或監測的屬性。
  • 設置和顯示自定義標籤的原子。
  • 顯示標籤顯示當前債券鍵長或當前計算量子力學的債券秩序。
  • 顯示蛋白骨幹使用緞帶,測試表,隨機線圈,缸等可選顯示側鏈。 
  • 突出潛在氫鍵相互作用。
  • 顯示偶極矩向量和梯度向量。

計算化學

利用 HyperChem的 探索量子或古典模型勢能面與單點,幾何優化,或過渡狀態搜索計算。 包括熱運動的影響與分子動力學,朗之萬動力學蒙特卡羅模擬或大都市。 用戶定義的結構限制可能被添加。

類型的計算

  • 單點計算確定的分子能量和屬性為給定的固定幾何形狀。 
  • 幾何優化計算,採用能量最小化算法來找到穩定的結構。 五是提供最小化算法。
  • 振動頻率計算,發現正常的振動模式的優化結構。 振動頻譜可以顯示和振動運動與特定的轉換可以是動畫。
  • 過渡態搜索定位到相應的亞穩結構過渡態或使用以下任一特徵向量同步交通方式。 然後計算出的分子特性。
  • 分子動力學模擬計算分子經典軌跡的系統。 量子力量可以被用來模擬反應碰撞。 暖氣,平衡,冷卻時間可受聘為模擬退火和溫度依賴性研究了其他進程。 恆定能量和恆溫模擬可用。
  • 朗之萬動力學模擬增加摩擦和隨機力量常規分子動力學模型碰撞效應無溶劑明確列入溶劑分子。
  • 大都會 蒙地卡羅 配置模擬樣品從統計樂團在給定的溫度和有益的探索是可能的配置的一個系統,以及不同溫度下的平衡計算平均數。
  • 通過激發態的單激發組態相互作用(CI)的。

計算方法

密度泛函理論(DFT)

  • 選擇一個種類繁多的交流和相關泛函。
  • 選擇從各種各樣的一體化電網
  • 所有的選項的從頭計算和基礎功能(見下文)。 

從頭計算 量子力學

  • 選擇許多常用的基礎設置(高級技術主任,1G到D95 **)包括標準高級技術主任和3G,3 21號,6 - 31G *水平和6 - 31G **基組
  • 額外的基礎功能(硫,磷,研發,藻,社民黨)可以添加到單個原子或原子的群體。
  • 用戶還可以定義自己的基礎上設置或修改現有的基礎上方便地使用組 HyperChem的的記載的基礎上設置文件格式。 

半經驗量子力學

  • ĤyperChem 提供11半經驗分子軌道方法,並與選擇有機及主要組化合物,過渡金屬配合物,光譜和模擬。
  • 選擇由擴展赫克,的CNDO,印度,明多/ 3,MNDO級別上的,的MNDO /天,的AM1,令吉,採用 PM3(包括過渡金屬),的ZINDO / 1和的ZINDO / S的

分子力學

  • 四力場提供方便的計算方法為探索穩定和動態的分子系統。
  • 新增用戶定義的靈活性原子類型和參數。
  • 選擇毫米,通用力場,和三個專業生物分子力場:琥珀,生物,和OPLS。

混合模式計算

  • HyperChem的 允許您執行量子計算的一個分子體系的一部分,如溶質,而其餘的治療系統經典。 這個邊界技術適用於所有的量子方法,並與一些限制的 從頭 計算。

自定義和擴展與 HyperChem的化驗師的開發工具包

  • 簡化 HyperChem的的菜單。 添加新的圖形和計算功能,創建自定義菜單的具體應用。
  • 界面到Visual Basic,C語言,C和FORTRAN程序。 添加對話框以及菜單項。 例如,您可以使用 HyperChem的 可視化結構和結果非圖形化的量子化學程序。
  • 鏈接 HyperChem的 程序,其他Windows程序,如MS Word和Excel,直接選擇的結果,以方便這些應用的分析和報告。










Features of HyperChem

 
 
   
 
 
  
 
 

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.
  • Replace any selected Hydrogen with a variety of substituents including your own custom substituent.
  • 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 molecular assemblies; 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 salvation 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, ball and cylinder, or tubes
  • Add van der Waals dots to any rendering.
  • Use any rendering on any atom in the same molecule. 
  • Specify stick or cylinder width, and the radii of spheres.
  • Stereo and perspective viewing are available as well as a quality setting.
  • 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, beta sheets, random coils, cylinders, etc. with optional display of side chains. 
  • 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.
  • Excited states via singly-excited configuration interaction (CI).

Computational Methods

Density Functional Theory (DFT)

  • Choose from a large variety of exchange and correlation functionals.
  • Choose from a variety of integration grids
  • All the options of Ab Initio calculations and basis functions (see below)

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 eleven 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, RM1, 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 computational features; 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 Excel; direct selected results to these applications for convenient analysis and reporting.