INTRODUKSI
Program HyperChem, merupakan program kimia aplikasi 32 bit, yang dikembangkan oleh HyperCube Inc untuk system operasi Windows 95/98 dan Windows NT. HyperChem merupakan program yang handal dari pemodelan molekul yang telah diakui mudah digunakan, fleksibel dan berkualitas. Dengan menggunakan visualisasi dan animasi tiga dimensi hasil perhitungan kimia kuantum, mekanika dan dinamika molekular, menjadikan HyperChem terasa sangat mudah digunakan dibandingkan dengan program kimia kuantum yang lain.
Program Kimia menyediakan fasilitas pembuatan model tiga dimensi (3D), perhitungan mekanika molekular dan mekanika kuantum (semiempiris dan ab initio). Disamping itu tersedia pula database dan program simulasi Monte Carlo dan molecular dynamics (MD).
Fasilitas yang disediakan oleh program standar ini adalah:
· Input Struktur dan Manipulasi (Structure Input and Mani-pulation)
· Display Molekul (Molecular Display)
· Kimia Komputasi (Computational Chemistry)
· Metode Komputasi (Computational Methods)
HASIL PERHITUNGAN DENGAN HYPERCHEM
Prediksi:
HyperChem dapat digunakan untuk menentukan bebe-rapa sifat struktur antara lain :
· Stabilitas relatif dari beberapa isomer · Panas pembentukan · Energi aktivasi · Muatan atom · Beda energi HOMO-LUMO · Potensial Ionisasi · Afinitas elektron · Momen dipol · Tingkat energi elektronik · Energi korelasi elektron MP2 | · Energi keadaan tereksitasi CI · Sifat dan struktur keadaan transisi · Energi interaksi non-bonded · Spektra serapan UV-VIS · Spektra Absorpsi IR · Pengaruh isotop pada vibrasi · Spektra serapan IR · Efek Collision pada sifat struktur · Stabilitas dari kluster |
Simulasi
- Interaksi Docking
- Pengaruh temperatur pada gerakan molekul
- Pengaruh pelarut pda struktur dan dinamika
- Interaksi intermolekular pada kluster
VIEW TOOLBARS STANDARD
Seketika HyperChem aktif, maka tampak toolbars standard berikut:
Beberapa toolbars yang harus dipahami dulu adalah Draw, Select, Rotate out-of-plane (XY Rotation), Rotate in-plane (Z Rotation), Translate (XY Translation), Z-Translate, Magnify/shrink/Zoom,Z-Clipping planes, dan Text Annotation. Penjelasannya sebagai berikut:
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: button `Drawing' untuk menampakkan sistem periodik unsur; cara melakukanya
Dengan klik 2 kali secara cepat: button `Selection' untuk memilih atom atau molekul atau untuk melihat panjang ikatan, sudut ikatan, dan sudut torsi
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: button `XY Rotation' untuk memutar molekul sekitar sumbu X dan Y
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: button `Z Rotation' untuk memutar molekul sekitar sumbu Z
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: button `XY Translation' untuk menggerakkan atom dan molekul sepanjang sumbu
X dan Y : button `Z Translation' untuk menggerakkan atom dan molekul sepanjang sumbu Z
: button `Zoom' untuk membesarkan atau mengecilkan sistem molekul. Caranya, tekan tombol kin mouse, gerakan ke kiri-bawah untuk membesarkan, atau gerakan ke kanan-atas untuk mengecilkan: button `Z Clipping' untuk memotong molekul
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: button `Text Annotation' untuk menambakkan text pada layar
Button toolbars yang lain adalah button standar pada Ms Office, yaitu
New : memulai file baru
Open : membuka file lama
Save : menyimpan file aktif ke disket/H-Disk
Cut : menghilangkan pilihan dan menyimpan ke memori
Copy : menyimpan pilihan ke memori
Paste : menempelkan simpanan di memori ke layar
Print : nge-printing
PERSIAPAN MEMBUAT FILE STRUKTUR BARU
Langkah sederhananya :
Klik <File>, pilih <Preferences>, sehingga muncul tampilan berikut
Pilih pada <Window Color> <White>, supaya layar HyperChem berwarna putih.
Pilihan lain pada <Preferences> dapat dicoba sendiri.
Klik <Display>, pilih <Labels>, sehingga muncul tampilan berikut:
Pada <Labels> pilihlah <Symbol> dalam <Atoms>, lalu pilihlah <Bond Order> dalam Bonds>. Sementara pilihan manut dulu, lain kali terserah.
MEMBUAT STRUKTUR BARU
Langkah mudahnya:
Klik <File> lalu pilih <New>, supaya layar bersih
Klik button [Draw] 
2 kali dengan cepat sehingga muncul < Element Tabel>
2 kali dengan cepat sehingga muncul < Element Tabel>
Seumpama akan membuat struktur etana (CH3CH3), maka klik I kali huruf <C> pada <Element Tabel>. Ingat pilihan <Explicit Hydrogens> pada <Element Tabel> jangan dicentang (tidak dipilih dulu)
Pada layar putih klik kiri mouse 1 kali, kemudian klik kiri mouse I kali lagi dekat dengan yang pertama, seperti pada gambar
Klik kiri mouse pada C sebelah kiri, jangan dilepas dulu klik kirinya, geser atau hubungkan ke C yang kedua, sehingga terbentuk ikatan, seperti gambar berikut
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Klik <Build> dan pilihlah <Add H & Model Build> sehingga muncul struktur berikut
Klik button toolbars yang lain untuk mengubah posisi stuktur, misalnya klik 1 kali button [XY Rotation] 
, kemudian pada layar putih klik kiri mouse dan tahan tents sambil menggeser mouse kesana-kemari. Coba pilihan lain, misal [translation], dan [zoom]
, kemudian pada layar putih klik kiri mouse dan tahan tents sambil menggeser mouse kesana-kemari. Coba pilihan lain, misal [translation], dan [zoom]MELIHAT PANJANG IKATAN, SUDUT IKATAN, DAN SUDUT TORSION
Klik <Select> dan pilihlah <Atoms>, untuk memilih atom-atom
Klik button toolbars [Select] 
1 kali saja
1 kali sajaUntuk melihat panjang ikatan, arahkan button [Select] pada garis ikatan tertentu, misalnya garis ikatan antar C, dan klik kiri mouse l kali tepat pada garis ikatan yang dipilih, maka akan muncul keterangan pada garis paling bawah layar seperti berikut ini
Jarak antar C adalah 1,54 Angstrom
Cobalah lagi pada garis ikatan lain, dan bacalah panjang ikatannya!
Untuk membebaskan kursor mouse dan memilih maka klik kanan mouse 1 kali di sembarang tempat.
4. Untuk melihat sudut ikatan H-C-H, maka klik kiri mouse dan tahan tepat di atas atom H pertama dan geserkan ke atom H kedua, lepaskan klik, dan lihat hasilnya.
Sudut antara atom nomer 6-2-7 (H-C-H) adalah 109,471°.
Coba antar 3 atom yang lain ! Misal sudut H-C-C !
5. Untuk melihat sudut torsi atom H-C-C-H, maka klik kiri mouse pada atom H pertama, tahan klik dan geserkan ke atom H kedua, sehingga muncul gambar berikut
Sudut torsi atom H-C-C-H adalah 180°
STRUKTUR 3 DIMENSI
Klik <Display>, dan pilihlah <Rendering>, muncul tampilan berikut
Pada Rendering Options terdapat berbagai pilihan : Rendering Method, Sticks, Balls, Cylinders, dan Overlapping Spheres. Misalkan pilihannya pada
Rendering Method : Balls and Cylinder
Sticks : Pilih semua, kecuali Stereo
Balls : Shading dan Highlight
Cylinder : Color by element
Overlapping Sphere : Shading dan Highlight
Maka akan diperoleh gambar 3 dimensi sebagai berikut:
Untuk berubah ke bentuk semula (misalnya Sticks) tinggal tekan tombol <F2>, bolak-balik!
Perlakukan bentuk gambar 3 dimensi ini seperti bentuk <Sticks>, misalkan untuk melihat panjang ikatan, sudut ikatan 3 atom, dan sudut torsi 4 atom pilihan. Gerakkan pula dengan <XY Rotation>, <Z Rotation>, <Translation>, atau <Zoom>
Untuk melihat gambar 3 dimensi yang bagus banget, maka klik <Display> dan pilihlah <Raytrace>
Jangan lupa simpan gambar strukturnya dengan memilih <File> dan <Save>, kemudian beri nama file (misal gambar 1).
MENGUBAH STRUKTUR MOLEKUL
Bagaimana membuat struktur Toluena dengan mengubah dari Benzena ?
Klik menu <File>, pilih <Open>, carilah file `Benzene' di direktori C:\Hyper80\ Samples\aromatic
Klik file `Benzene' dan <Open>, maka akan muncul struktur Benzena
Klik menu <Select> dan pilih <Atoms>, ingat jangan pilih dulu <Multiple Selections>, karena hanya akan memilih satu pilihan saja
Klik kiri mouse tepat di atas salah satu atom H sampai ada tanda lingkaran, tanda berhasil memilih, kemudian pilih tombol <Delete> pada keyboard
Klik button [Draw] 
2 kali dengan cepat sehingga muncul <Element Tabel>
2 kali dengan cepat sehingga muncul <Element Tabel>Klik 1 kali huruf <C> pada <Element Tabel>
Klik kiri mouse l kali tepat pada posisi atom H yang dihapus
Tarik garis ikatan dari atom C baru ke atom C yang dihilangkan atom H-nya, dengan cara menekan tombol kiri mouse tepat di atas atom C baru, tahan dan geserkan ke atom C yang hilang atom H-nya
Klik <Build> dan pilihlah <Add H & Model Build>
Klik button [XY Rotation] dan gerakan molekul sehingga atom H yang lain tampak
dan gerakan molekul sehingga atom H yang lain tampakMEMBUAT STRUKTUR MOLEKUL DART CS CHEMDRAW ULTRA
Aktifkan program CS ChemDraw Ultra
Klik button tool text 
1 kali
1 kaliMisal akan membuat struktur TNT (Trinitrotoluene), klik kiri mouse di ruang kosong, kemudian ketik `trinitrotoluene' (harus istilah asing)
Klik button tool Marquee 
1 kali saja
1 kali sajaKlik menu <Structure>, kemudian pilihlah <Convert Name to Structure>, maka akan keluar struktur TNT
Klik button tool Marquee kemudian lakukan blok terhadap struktur TNT (nama struktur jangan ikut diblok),
kemudian lakukan blok terhadap struktur TNT (nama struktur jangan ikut diblok),Klik menu <Edit>, pilihlah <Copy>
Aktifkan program HyperChem
Klik <File>, pilihlah <New> untuk membersihkan ruang
Klik <Edit>, pilihlah <Paste>, maka akan muncul struktur TNT
Simpanlah dan beri nama file ‘TNT’
Cobalah sendiri cara ini untuk membuat struktur `Picric acid' atau `2,4,6-trinitrophenol', `Ammonium picrate', dan `2,4,6-trinitrophenyl-methylnitramine' pada program HyperChem melalui CS ChemDraw Ultra
MENGAMBIL FILE STRUKTUR MOLEKUL DART DATABASE
Program HyperChem menyediakan database untuk beberapa struktur molekul, diantaranya struktur asam-asam amino, asam nukleat, kristal, sakarida dan struktur lain. Caranya sebagai berikut:
Klik menu <Databases>, pilih <Amino acids>, maka akan muncul kotak dialog beberapa nama asam amino, pilihlah salah Satu.
Klik menu <Databases>, pilih <Saccharides>, klik <Add>, maka akan muncul kotak dialog beberapa jenis sakarida, pilih salah satu, misalnya <aldoses>, <ketoses> atau yang lain
Contoh prosedur untuk sugar dan crystal sebagai berikut:
Procedure: Sugar Builder (Databases Menu)
The Sugar (Polysaccharide) Builder module is invoked by a simple click on the HyperChem menu item. The module has its own structure, menus, and dialog boxes. See the manuals for a more complete description of the Sugar Builder Module.
Invoking the Sugar Builder Module
L-click on Databases/Saccharides
Creating poly (1->4)--D-Glucose
L-click on Databases/Saccharides
Use the Add/Aldoses menu command to bring up the Aldoses dialog box.
Select the D and options to select the D isomer and anomer.
Choose the Glucose command button to create a glucose residue in HyperChem.
Choose the 14 connection type by selecting it from the list.
Change f and y to 48.05 and -20 by entering these numbers in their edit boxes, respectively.
Repeatedly click on the Glucose command button, once for each residue you wish to add to the chain.
L-click in the upper right-hand corner of the Aldoses dialog box and the Sugar Builder Module to close the sugar builder.
Switch back to HyperChem to view the polysaccharide.
Procedure: Crystal Builder (Databases Menu)
The Crystal Builder module is invoked by a simple click on the HyperChem menu item. The module has is own structure, menus, and dialog boxes. See the manuals for a more complete description of the Crystal Builder Module.
Invoking the Crystal Builder Module
L-click on Databases/Crystals
Creating a Molecular Crystal
Create a molecule in HyperChem
L-click on Databases/Crystals
L-click on HyperChem/Get in the Crystal Builder Module
Select the Crystal Type, Unit Cell Parameters and the Number of Unit Cells in the Crystal Builder Module
L-click on HyperChem/Put in the Crystal Bulder Module
Close the Crystal Builder Module by an L-click in the upper right-hand corner.
Return to HyperChem
Reading in a Molecule from the Cambridge Crystallographic Database
L-click on Databases/Crystals to bring up the Crystal Builder Module
L-click on File/Open in the Crystal Builder Module
Navigate to an appropriate directory and read in a CSD file
L-click on HyperChem/Put in the Crystal Builder Module
Close the Crystal Binder Module by an L-click in the upper right-hand corner.
Return to H
METODE KOMPUTASI
Struktur yang pertama kali dibuat mungkin belum optimal geometri strukturnya, karena itu harus dilakukan optimasi geometri untuk menempatkan konformasi yang stabil menggunakan metode komputasi tertentu. HyperChem telah menyediakan dalam menu <Setup>. Sebagai gambaran berikut ini dijelaskan secara singkat metode komputasinya.
Metode Kimia Komputasi
Metode kimia komputasi dapat dibedakan menjadi 2 bagian besar yaitu mekanika molekuler dan metode struktur elektronik yang terdiri dari metode semiempiris dan metode ab initio. Metode yang sekarang berkembang pesat adalah teori kerapatan fungsional (density functional theory, DFT).
Banyak aspek dinamik dan struktur molekul dapat dimodelkan menggunakan metode klasik dalam bentuk dinamik dan mekanika molekul. Medan gaya (force field) klasik didasarkan pada hasil empiris yang merupakan nilai rata-rata dari sejumlah besar data parameter molekul. Karena melibatkan data dalam jumlah besar hasilnya baik untuk sistem standar, namun demikian banyak pertanyaan penting dalam kimia yang tidak dapat semuanya terjawab dengan pendekatan empiris. Jika ada keinginan untuk mengetahui lebih jauh tentang struktur atau sifat lain yang bergantung pada distribusi kepadatan elektron, maka penyelesaiannya harus didasarkan pada pendekatan yang lebih teliti dan bersifat umum yaitu kimia kuantum. Pendekatan ini juga dapat menyelesaikan permasalahan non-standar, yang pada umumnya metode mekanika molekuler tidak dapat diaplikasikan.
Kimia kuantum didasarkan pada postulat mekanika kuantum. Dalam kimia kuantum, sistem digambarkan sebagai fungsi gelombang yang dapat diperoleh dengan menyelesaikan persamaan Schrödinger. Persamaan ini berkait dengan sistem dalam keadaan stasioner dan energi mereka dinyatakan dalam operator Hamiltonian. Operator Hamiltonian dapat dilihat sebagai aturan untuk mendapatkan energi terasosiasi dengan sebuah fungsi gelombang yang menggambarkan posisi dari inti atom dan elektron dalam sistem. Dalam prakteknya, persamaan Schrödinger tidak dapat diselesaikan secara eksak sehingga beberapa pendekatan harus dibuat. Pendekatan dinamakan ab initio jika metode tersebut dibuat tanpa menggunakan data empiris, kecuali untuk tetapan dasar seperti massa elektron dan tetapan Planck yang diperlukan untuk sampai pada prediksi numerik. Jangan mengartikan kata ab initio sebagai penyelesaian eksak. Teori ab initio adalah sebuah konsep perhitungan yang bersifat umum dari penyelesaian persamaan Schrödinger yang secara praktis dapat diprediksi tentang keakuratan dan kesalahannya.
Kelemahan metode ab initio adalah kebutuhan yang besar terhadap kemampuan dan kecepatan komputer. Dengan demikian penyederhanaan perhitungan dapat dimasukkan ke dalam metode ab initio dengan menggunakan beberapa parameter empiris sehingga dihasilkan metode kimia komputasi baru yang dikenal dengan semiempiris. Metode semiempiris dapat diterapkan dalam sistem yang besar dan menghasilkan fungsi gelombang elektronik yang baik sehingga sifat elektronik dapat diprediksi. Dibandingkan dengan perhitungan ab initio, realibilitas metode semiempiris agak rendah dan penerapan metode semiempiris bergantung pada ketersediaan parameter empiris seperti halnya pada mekanika molekul.
Skema Pembagian Metode Kimia Komputasi.
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Skema Karakterisasi Metode Kimia Komputasi
Metode Mekanika Molekuler
Metode mekanika molekuler menyediakan pernyataan aljabar yang sederhana untuk energi total senyawa, tanpa harus menghitung fungsi gelombang atau kerapatan elektron total. Pernyataan energi mengandung persamaan klasik sederhana, seperti persamaan osilator harmonis untuk menggambarkan energi yang tercakup pada terjadinya uluran, bengkokan dan torsi ikatan, gaya antar molekul seperti interaksi van der waals dan ikatan hidrogen.
Dalam metode mekanika molekular, data base senyawa yang digunakan dalam metode parameterisasi merupakan hal yang krusial berkaitan dengan kesuksesan perhitungan. Himpunan parameter dan fungsi matematika dinamakan medan gaya (force-field).
Dibandingkan dengan metode-metode kimia komputasi yang lain, metode mekanika molekuler mempunyai sisi baik dan sisi buruk. Sisi baik dari mekanika molekuler adalah dimungkinkannya modeling terhadap molekul yang besar seperti halnya protein dan segmen dari DNA tanpa kapasitas komputer yang besar dengan proses perhitungan komputer yang tidak terlalu lama. Sedangkan metode komputasi yang lain juga mampu modeling terhadap molekul besar namun memerlukan kapasitas komputer yang besar dan proses perhitungannya memerlukan waktu yang lama. Sisi buruk dari mekanika molekular adalah banyak sifat kimia yang tidak dapat didefinisikan dengan metoda ini. Misalnya dalam proses dan hasil perhitungan. Metode mekanika molekuler hanya mampu memvisualisasikan perhitungan energi total tetapi pada metode semi empiris selain memvisualisasikan perhitungan energi total juga mampu memvisualisasikan perhitungan panas pembentukan.
Mekanika molekul dikembangkan untuk mendiskripsikan struktur dan sifat-sifat molekul sesederhana mungkin. Bidang aplikasi mekanika molekular meliputi :
Molekul yang tersusun oleh ribuan atom.
Molekul organik, oligonukleotida, peptida dan sakarida.
Molekul dalam lingkungan vakum atau berada dalam pelarut.
Senyawa dalam keadaan dasar.
Sifat-sifat termodinamika dan kinetika.
Beberapa jenis medan gaya yang sering digunakan dalam kimia komputasi pada metode mekanika molekuler :
· MM+ (Sesuai untuk sebagian besar spesies non-biologi).
· AMBER (Sesuai digunakan dalam polipeptida dan asam nukleat dengan semua atom hidrogen diikutkan dalam perhitungan).
· BIO+ (Dikhususkan untuk perhitungan molekul protein).
· OPLS (Metode yang juga dikembangkan untuk protein, tetapi perhitungan interaksi non-ikatannya lebih akurat dari metode AMBER).
Beberapa kalkulasi pada menu <Compute> yang dapat dilakukan oleh Mekanika Molekuler adalah : Single Point, Geometry Optimization, Moleculer Dynamics Simulation, Langevin Dynamics Simulation, Monte Carlo Simulation, Conformational Search, dan QSAR Properties.
Quantum mechanics
A theory of electron movement and interactions based on the recognitions that electrons travel in a limited number of orbits around an atomic nucleus, and that each orbit is characterized by a specific radius and energy. Electrons can move from one orbit to another by absorbing or emitting discrete packets of energy, known as quanta. Moving electrons have the properties of both particles and waves and an orbital using the wave aspect to describe the probability of finding an electron at a particular point in space. The Schrodinger equation and its derivatives describe completely the behavior of electrons relative to a fixed nucleus. Using these equations, it is possible to accurately describe electrons and the behavior of chemical compounds. Semi-empirical calculations in HyperChem use approximate solutions of the Schrodinger equation, plus empirical data (parameters), to predict electronic properties of molecular systems. Ab initio calculations use different approximations to the Schrodinger equation, without empirical parameters.
Semi-empirical
A type of quantum mechanics chemical calculation that uses parameters derived from experiments to simplify the calculation process.
Script Variable: semi-empirical-method
Type: enum (extendedhuckel, cndo, indo, mindo3, mndo, am1, pm3, zindo1, zindos)
Read Write Status: R, W
Use: Sets in the type of semi-empirical quantum mechanism method for calculations.
Huckel
A simple and approximate method for semi-empirical quantum mechanics calculations. The Extended Huckel method used in HyperChem is useful only for single part calculations, not for geometry optimization or molecular dynamic calculations. Extended Huckel calculations produce qualitative or semi-quantitative descriptions of molecular orbitals and electronic properties (for example, net atomic charges and spin distributions). This is not a Self-Consistent Feb (SCF) method.
CNDO
Complete Neglect of Differential Overlap (see NDO). This is the simplest of the SCF methods for semi-empirical quantum mechanics calculations. It is useful for calculating ground state electronic properties of open- and closed-shell systems, geometry optimization, and total energy. HyperChem uses CNDO/2.
INDO
Intermediate Neglect of Differential Overlap (see NDO). This is an SCF method for semi-empirical quantum mechanics calculations. It improves on CNDO by accounting for certain one-center repulsions between electrons on the same atom. Useful for calculating ground-state electronic properties of open-and closed-shell systems, geometry optimizations, and total energy.
MINDO/3
Modified Intermediate Neglect of Differential Overlap. This is an SCF method for semi-empirical quantum mechanics calculations. An extension of INDO, MINDO/3 uses parameters fit to experimental results, instead of accurate calculations. Useful for large organic molecules, cations, and polynitro compounds. Calculates electronic properties, geometry optimizations, and total energy.
MNDO
Modified Neglect of Diatomic Overlap. This is an SCF method for semi-empirical quantum mechanics calculations. Useful for various organic molecules containing elements from long rows 1 and 2 of the periodic table, but not transition metals. Eliminates some errors in MNDO/3. Calculates electronic properties, optimized geometries, total energy, and heat of formation.
AM1
A semi-empirical SCF method for chemical calculations. An improvement of the MNDO method. Useful for molecules containing elements from long rows 1 and 2 of the periodic table, but not transition metals. Together with PM3, AM1 is generally the most accurate semi-empirical method included in HyperChem. Calculates electronic properties, optimized geometries, total energy, and heat of formation.
PM3
A semi-empirical SCF method for chemical calculations. PM3 is a reparametrization of the AM1 method. PM3 and AM1 are generally the most accurate methods in HyperChem. PM3 has been parameterized for many main group elements and some transition metals.
ZINDO/1
Based on a modified version ofINDO/1. You can use ZINDO/1 for calculating energy states in molecules containing transition metals.
ZINDO/S
An INDO method parameterized to reproduce UV visible spectroscopic transitions when used with singly-excited configuration interaction (CI) methods.
Use ZINDO/1 rather than ZINDO/S for geometry optimizations and comparisons of total energies.
Beberapa komputasi pada menu <Compute> yang dapat dilakukan oleh Semi Empiric, selain metode Extended Huckel adalah : Single Point, Geometry Optimization, Moleculer Dynamics Simulation, Langevin Dynamics Simulation, Monte Carlo Simulation, Vibrations, Transition State, Conformational Search, dan QSAR Properties.
Sedangkan metode Extended Huckel hanya dapat untuk : Single Point, Conformational Search, dan QSAR Properties.
Ab initio method
Perhitungan komputasi dinamakan ab initio jika metode tersebut dibuat tanpa menggunakan data empiris, kecuali untuk tetapan dasar seperti massa elektron dan tetapan Planck yang diperlukan untuk sampai pada prediksi numerik. Metode ab initio tidak dapat disebut penyelesaian eksak. Teori ab initio adalah sebuah konsep perhitungan yang bersifat umum dari penyelesaian persamaan Schrödinger yang secara praktis dapat diprediksi tentang keakuratan dan kesalahannya. Kelemahan metode ab initio adalah kebutuhan yang besar terhadap kemampuan dan kecepatan komputer.
Ab initio calculations can be performed at the Hartree-Fock level of approximation, equivalent to a self-consistent-field (SCF) calculation. The post Hartree-Fock level includes the effects of correlation which are not inducted at the Hartree-Fock level of approximation of a non-relativistic solution to the Schrodinger equation (within the clamped-nuclei Born-Oppenheimer approximation).
HyperChem performs ab initio SCF calculations generally. It also can calculate the correlation energy (to be added to the total SCF energy) by a post Hartree-Fock procedure call MP2 that does a Mailer-Plesset second-order perturbation calculation. The MP2 procedure is only available for single point calculations and only produces a single number, the MP2 correlation energy, to be added to the total SCF energy at that single point configuration of the nuclei.
Basis set
Any set of one-electron functions can be a basis set in the LCAO approximation. However, a well-defined basis set will predict electronic properties using fewer terms than a poorly-defined basis set. Thus, choosing a proper basis set in ab initio calcuations is critical to the rellability and accuracy of the calculated results.
One would like to define, in advance, the standard basis sets that will be suitable to most users. However, one also wants to allow sophisticated users the capability to modify existing basis sets or to define their own basis sets. We have thus defined a HyperChem basis set file format, and the HyperChem package includes a number of these. BAS files that define standard basis sets. Users can also define as many of their own basis sets as they like using this file format. The details of the HyperChem basis sets file format are described in Chapter 6 of the HyperChem Release 4.5 New Features manual.
Many conventional and commonly-used ab initio basis sets are supported in HyperChem. These basis sets include:
STO-1G and STO-1G* (H and He);
STO-2G and STO-2G* (H to Xe);
STO-3G and STO-3G* (H to Xe);
STO-4G and STO-4G* (H to Xe);
STO-5G and STO-5G* (H to Xe);
STO-6G and STO-6G* (H to Xe);
3-21G, 3-21G*, and 3-21G** (H to Ar);
4-21G, 4-21G*, and 4-21G** (H to Ne);
6-21G, 6-21G*, and 6-21G** (H to Ar);
4-31G, 4-31G*, and 4-31G** (H to Ne);
5-31G, 5-31G*, and 5-31G** (H to F);
6-31G, 6-31G*, and 6-31G** (H to Ar);
6-311G, 6-311G*, and 6-311G** (H to Ar);
D95, D95* and D95** (H to CI).
Beberapa komputasi pada menu <Compute> yang dapat dilakukan oleh Ab Initio adalah : Single Point, Geometry Optimization, Moleculer Dynamics Simulation, Langevin Dynamics Simulation, Monte Carlo Simulation, Vibrations, Transition State, Conformational Search, dan QSAR Properties.
OPTIMASI GEOMETRI STRUKTUR MOLEKUL
Menu Activator: maenu-compute-geometry-optimization
Use: Finds an optimal conformation for the molecular system.
Dialog Box: Molecular Mechanics or Semi-empirical or ab initio Geometry Optimization
Langkah persiapan sebelum komputasi adalah menyiapkan file tempat menyimpan data hasil komputasi. Caranya adalah :
Klik <File>, pilihlah <Start Log>, tentukan direktori file-nya, contohnya di `My Documents', kemudian beri ’nama file' dan klik <OK>
Siap melaksanakan penyimpanan hasil komputasi
Optimasi Geometri
Sebagaimana kita ketahui, perubahan struktur dalam suatu molekul biasanya menghasilkan perbedaan energi dan sifat-sifat lainnya. Oleh karena itu perhitungan-perhitungan penyelidikan dilakukan pada suatu sistem molekul yang memiliki struktur geometri yang tertentu. Bagaimana energi suatu sistem molekul berubah sejalan dengan perubahan kecil pada strukturnya digambarkan oleh energi potensial permukaannya.
Inti prosedur optimasi suatu struktur molekul adalah membandingkan energi struktur yang didapatkan dengan struktur sebelumnya. Energi struktur yang lebih rendah dari sebelumnya menunjukkan kestabilan struktur dibandingkan sebelumnya. Prosedur ini diulang sampai mendapatkan energi struktur yang tidak jauh berbeda dengan sebelumnya.
Penentuan struktur yang stabil dari molekul merupakan langkah perhitungan yang paling umum terjadi pada pemodelan molekul. Energi relatif dari struktur teroptimasi yang berbeda akan menentukan kestabilan konformasi, keseimbangan isomerisasi, panas reaksi, produk reaksi, dan banyak aspek lain dari kimia.
Ada 4 jenis metode optimasi yang sering digunakan, yaitu :
Steepest descent, dikhususkan untuk perhitungan yang cepat agar menghilangkan sterik yang berlebihan dan masalah tolakan pada struktur awal.
Conjugate gradient Fletcher-Reeves untuk mencapai konvergensi yang efisien.
Conjugate gradient Polak-Riebere hampir sama dengan metode Fletcher-Reeves, yaitu untuk mencapai konvergensi yang efisien
Block-diagonal Newton-Raphson (hanya untuk MM+), yang memindahkan satu atom pada suatu waktu dengan menggunakan informasi turunan keduanya.
Algoritma Conjugate gradient lebih baik digunakan dibandingkan dengan algoritma Steepest descent. Perbedaan terdapat pada metode perhitungannya.
Langkah-langkah optimasi
Select the atoms for optimization, or deselect all atoms to optimize the whole molecular system.
Specify either Sctup/Molecular Mechanics or Setup/Semi-empirical.
Select Compute/Geometry Optimization.
Specify the algorithm used to calculate the minimum potential energy.
Algorithm
Specify the options for the calculations.
Options
Specify how often to refresh the screen by entering a number in the Screen refresh period text box.
L-click OK.
Algorithm
Steepest Descent
Moves directly down the steepest slope of interatomic forces on the potential energy surface, making limited changes to the molecular structure. This method is useful for correcting bad geometry or removing bad contacts. It is most effective when the molecular system is far from minimum, and is less satisfactory for macromolecular systems.
Fletcher-Reeves
A conjugate gradient method using one-dimensional searches. This algorithm converges better than the Steepest Descent method.
Polak-Ribiere
A conjugate gradient method using one-dimensional searches, converging more quickly than Fletcher-Reeves but using slightly more memory.
Eigenvector-Following
Available for semi-empirical and ab initio quantum mechanical methods (Setup/Semi-empirical and Setup/Ab initio), this method moves the atoms of a molecular system based on the eigenvector of the Hessian (the second derivatives of the total energy with respect to displacements). The initial guess of the Hessian is computed empirically.
Block-diagonal Newton Raphson
Available for the MM+ force field, this method moves one atom at a time using second derivatives.
Options
Termination Conditions
HMS gradient
Set the root-mean-square (RMS) gradient to determine the end of the calculations. When the RMS gradient is less than the value you enter, the calculation ends.
Cycles Enter a number to limit the number of search directions. The default value is 15 times the number of atoms.
In vacuo Removes the periodic boundaries from the calculation.
Periodic boundary conditions
Uses the periodic boundary conditions that exist for the molecular system. You can turn this off by specifying In Vacuo.
Optimasi geometri minimal dapat juga dilakukan dengan menggunakan <Single Point> dari menu <Compute>. Metode yang dipilih dapat Molecular Mechanics, Semi-empirical, atau Ab Initio pada menu <Setup>.
Single point
A calculation that determines the total energy (in Kcal/mole) and gradient of a molecular system or of selected atoms. With a semi-empirical or ab Initio method, a single point calculation also determines the electron (charge) distribution in the system. The calculation represents only the present molecular configuration, a single point on the energy surface for the molecular system.
Procedure: Ab Initio Single Point (Compute Menu)
Computing a single point using the anti ama5iaa method
Select the atoms to include in the calculation, or deselect all atoms to perform calculations on the whole molecular system.
Select Setup/Ab Initio.
Set the options you want in the Ab Initio Options dialog box.
Select Compute/Single point.
Choose either of the following options:
Hasil komputasinya dapat dilihat pada lampiran 1.
SIMULASI GERAKAN MOLEKUL
Melihat simulasi gerakan molekul dapat dilakukan menggunakan menu <Compute> dengan pilihan <Molecular Dynamics> atau <Langevin Dynamics> atau <Monte Carlo>.
Molecular dynamics
Calculations that simulate the motion of each atom in a molecular system at a fixed energy, fixed temperature, or with controlled temperature changes. The result of molecular dynamics calculation is called a trajectory. HyperChem can use any one of the molecular mechanics semi-empirical quantum mechanics, or ab initio quantum mechanics method for a molecular dynamics trajectory. You can use this calculation to derive a large number of structural and thermodynamic properties, including alternative local minima, energy differences between different configurations, and reaction mechanisms and pathways.
Langeren Dynamics
Calculates the motion of selected stairs or all atoms in a molecular system, over picosecond time intervals. Demonstrates stable conformations, transition states, and thermodynamic properties. Use either a molecular mechanics or semi-empirical or ab initio method. Uses frictional effects to simulate the presence of a solvent.
You perform Langevin Dynamics calculations with HyperChem in the same way as you do Molecular Dynamics calculations. All of the dialog boxes for Langevin Dynamics are the same as for Molecular Dynamics except that a few of the available options are different. The Langevin Dynamics Options dialog box allows you to specify a Friction coefficient which describes the effects of the simulated solvent, and a Random seed which is the starting point for the random number generator.
Monte Carlo
Simulates molecular movement so that you can observe equilibrium properties and kinetic behavior. You can specify as many as three phases for the simulations – heating, running and cooling
Berikut ini prosedur kalkulasi Molecular Dynamics yang dapat juga dipakai untuk Langevin Dynamics dan Monte Carlo.
Calculating molecular dynamics
Select the atoms for molecular dynamics or deselect all atoms to simulate the whole molecular system.
Specify either Setup/Molecular Mechanics or Setup/Semi-empirical.
Select Compute/Molecular Dynamics.
Specify the Time Options.
Time Options
Specify the Temperature Options.
Temperature Options
Specify the other Options
Options
Select the output periods.
Data collection period
Screen refresh period
L-click the Playback or Restart option, if desired.
Playback
Restart
If you want snapshots so that you can later replay the simulation, L-click the Snapshots button.
Snapshots
Playback
If you want to calculate or plot averages, L-click the Averages button.
Averages
L-click the Proceed button in the Molecular Dynamics Options dialog box.
Simulasi gerakan molekul memakan waktu yang lama. Untuk menghentikan tekan menu <Cancel>.
ANALISIS VIBRASI
Vibrations command computes the vibrational motions of the nuclei and displays the normal modes associated with individual and infrared vibrations. You can use any of the semi-empirical methods except Extended Huckel, or any ab initio method except MP2.
Use <Vibrational Spectrum> on the <Compute> menu to view the results of the computation. Use vibrational analysis to perform the following tasks:
Provide insight into the rigidity of the molecular framework.
Visualize normal modes corresponding to lines in the IR spectrum.
Help identify unknown compounds by correlating predicted versus experimental vibrational frequencies.
Differentiate minima from saddle points on a potential energy surface.
Procedure: Vibrational Analysis (Compute Menu)
Draw the 2D structure: ethanol
Invoke the Model Builder to create a symmetric linear structure.
Choose <Semi-empirical> from the <Setup> menu. Use Vibrations only with semi-empirical methods for evaluating the energy.
Choose any semi-empirical method, except extended Huckel method.
Choose Options.
Set the options you want.
Choose <CI> to open the Configuration Interaction dialog box. Make sure None is selected as the CI Method. You cannot perform a geometry optimization with a CI wavefunction in HyperChem.
Close all of the open dialog boxes.
Choose Geometry Optimization on the Compute menu.
Vibrational analysis must be performed at a stationary point where the potential energy surface (PES) is defined by a zero gradient.
You must use the same semi-empirical method for both the vibrational analysis and the geometry optimization. For example, performing a vibrational analysis using the PM3 Hamiltonian at a geometry optimized using a CNDO Hamiltonian will generally be invalid
Choose the optimization you want.
After the calculation finishes, choose <Vibrations> on the <Compute> menu.
HyperChem computes the SCF wavefunction and evaluates the gradient analytically at the optimized geometry. The second derivatives of the energy with respect to the atomic
Cartesian coordinates are computed using a finite differencing of the analytical gradients.
The evaluation of the second derivatives are the most time consuming step. The result is a matrix of mixed partial second derivatives (force constants), which is diagonalized to yield normal modes of vibration and their corresponding energies. The status bar shows the extend to which the matrix is completed.
The normal modes represent a linear combination of atomic Cartesian displacements.
Choose <Vibrational Spectrum> from the <Compute> menu.
The Vibrational Spectrum dialog box, which shows the spectrum of frequencies corresponding to each normal mode. The spectrum (vertical lines) at the top represent all the vibrational fundamental frequencies. The spectrum at the bottom corresponds to IR-active vibrations. The frequency increases from the right side to the left side of the dialog box. The height of the bottom row of lines corresponds to their IR intensities.
Untuk melihat gerakan molekul tekan <Apply>, kalau molekul tertutup maka geser dulu kotak spektrum IR-nya dengan klik kiri mouse pada baris biru kotak dialog, tahan dan geserkan mouse sampai tidak menutupi molekul.
Tambahan nih : Supaya Spektrum IR dapat dicopy ke Ms Word maka klik <Copy>, coba aktifkan Ms Word atau Paint, dan klik <Edit>, lalu pilihlah <Paste>.
Untuk melihat data hasil komputasi sebelumnya dan spektrum IR maka klik <File>, lalu pilihlah <Stop Log>. Bukalah dengan Ms Word, asal ingat tempat direktori dan nama filenya (*.log). Ingat!! Langkah <Stop Log> dapat dilakukan kalau sebelum melakukan komputasi telah di-klik <Start Log> dari menu <File> dan sudah diberi nama file-nya.
Procedure: Transition State
Draw the 2D structure, say, methanol:
Double-click on the Selection tool icon. HyperChem builds the molecule.
Choose <Semi-empirical> on the <Setup> menu.
Choose a Semi-empirical method, say, <AM1> for a transition state calculation.
Compute/Transition State is not available for Extended-Huckel calculations.
Choose <Options>.
Set the Total charge, sat, 0, and the Spin multiplicity, say, 1, and then choose <OK> to close both dialog boxes.
Choose <Transition State> on the <Compute> menu.
The Transition State Search Options dialog box appears.
Choose the <Eigenvector Following a vibrational> mode radio button and L-click <OK>. This command starts a AM 1 calculation for the initial Hessian and vibrational modes for METHANOL. Wait until the calculation is done.
Select a vibrational mode, say, 1 from the Vibrational Modes dialog box and L-click OK. This tells HyperChem search a transition state by maximizing the energy along this specified mode and minimizing the energy along all other modes.
Wait until this calculation is done.
Choose <Vibrations> on the <Compute> menu.
This starts a vibrational calculation with the molecular system, methanol here.
Choose <Vibrational Spectrum> on the <Compute> menu.
The Vibrational Spectrum dialog box, which shows the spectrum of frequencies corresponding to each normal mode. The spectrum (vertical lines) at the top represent all the vibrational fundamental frequencies. The spectrum at the bottom corresponds to IR-active vibrations. The frequency increases from the right side to the left side of the dialog box. The height of the bottom row of lines corresponds to their IR intensities.
L-click the first vibrational mode (the first mode on the right side of the Vibrational Spectrum dialog box) to see the frequency of this vibrational mode.
L-click the second vibrational mode to the frequency of this vibrational mode.
If the frequency of the first vibrational mode is negative and the frequency of the second vibrational mode is positive, the molecular system is at a transition state. Otherwise, it is just at a stationary point, not a transition state.
Procedure: Transition State: Synchronous Transit Mode (Compute Menu)
Draw 2D structure that represents the product of a chemical reaction, say, CH3CH2C1
Double-click on the Selection tool icon. HyperChem builds the molecule.
Choose File/Save As to save the product to a file.
Draw another 2D structure that represents the reactant of the chemical reaction, say, CH2=CH2, and H-Cl
Double-click on the Selection tool icon. HyperChem builds the molecule.
L-click the Select tool from the Tool bar in HyperChem.
Select all the atoms in the reactant.
Choose Select/Name Selection.
The Name Selection dialog box appears.
L-click the REACTANT radio button and L-click.
Deselect the current selection and select all the atoms in the product.
Choose Select/Name Selection.
L-click the PRODUCT radio button and L-click OK.
Choose Setup/Reaction Map.
The Reaction Mapping dialog box appears.
Map the atoms in the reactant and the atoms in the product.
L-click OK once you have finished the mappings.
HyperChem closes the Reaction Mapping dialog box and creates an initial guess structure for a transition state search from the given reactant and product and the lamda value.
Choose Semi-empirical on the Setup menu.
Choose a Semi-empirical method, say, AM I for a transition state calculation.
Compute/Transition State is not available for Extended-Huckel calculations.
Choose Options.
Set the Total charge, sat, 0, and the Spin multiplicity, say, 1, and then choose OK to close both dialog boxes.
Choose the Synchronous Transit radio button and the QST radio button and L-click OK. This command starts a AMI calculation of searching a transition state. Wait until the calculation is done.
Choose Vibrations on the Compute menu.
This starts a vibrational calculation with the molecular system shown in the HyperChem workspace.
Choose Vibrational Spectrum on the Compute menu.
The Vibrational Spectrum dialog box, which shows the spectrum of frequencies corresponding to each normal mode. The spectrum (vertical lines) at the top represent all the vibrational fundamental frequencies. The spectrum at the bottom corresponds to IR-active vibrations. The frequency increases from the right side to the left side of the dialog box. The height of the bottom row of lines corresponds to their IR intensities.
L-click the first vibrational mode (the first mode on the right side of the Vibrational Spectrum dialog box) to see the frequency of this vibrational mode.
L-click the second vibrational mode to the frequency of this vibrational mode.
If the frequency of the first vibrational mode is negative and the frequency of the second vibrational mode is positive, the molecular system is at a transition state. Otherwise, it is just at a stationary point, not a transition state
ANALISIS SIFAT MOLEKUL
Procedure: Properties of Atom, Bond, or Molecular System
To display an atom’s properties
Select only one atom
L-click on Compute/Properties.
To display a bond's properties
Select only the two atoms of a bond.
L-click on Compute/Properties
To display the properties of the molecular system
See that nothing is selected (R-click with selection cursor in empty space), for NH3
L-click on Compute/Properties.
QSAR Properties
Properties calculated for Quantitative Structure Activity Relationships (QSAR). HyperChem calculates a number of properties rapidly that can then be used in QSAR studies. HyperChem does not directly do the QSAR with the calculated properties. The properties that can be calculated and are related to QSAR studies are:
Partial atomic charges - Gasteiger and Marsili scheme.
Surface areas - a grid method or a faster more approximate method. Either solvent accessible area or van der Waals surface area.
Hydration energy - for peptides and proteins
Volume - a grid method
Log P - according to Ghose, Pritvchett and Crippen
Refractivity - similar approach as for Log P
Mass - ordinary molecular mass
Procedure: QSAR Properties (Compute Menu)
Calculating QSAR Properties
Be sure you have a molecular system in the workspace
L-click on <Compute>, pilihlah <QSAR Properties>.
L-click on <Options> dan pilih <Output To..>
Select the Destinations for your results. Also decide whether you want to see atomic contributions.
L-click on one of the buttons to select one of the nine properties to calculate.
L-click on <Options> dan <Calculation Options> if it is enabled (un-grayed) for your property of interest and select any additional options.
If you are calculating Partial Charges, decide whether to use initial guesses of zero or to Base (the initial guess) on Current Charges.
L-click on the <Compute> button to calculate a QSAR property for the molecule in the workspace.
Electronic Spectrum
Computes the energy difference between the ground electronic state and the first few excited electronic states of a molecular system. ZINDO/S is specifically parameterized to reproduce ultraviolet-visible or “electronic” spectra; however, you can use any of the semi-empirical methods except Extended Huckel, or any of the ab initio methods except MP2.
You must perform a singly-excited CI method with the semi-empirical or ab initio method you choose in order to generate a UV-vis spectrum.
Procedure: Electronic Spectrum (Compute Menu)
Use the following procedure for UV visible spectroscopy:
Draw the two-dimensional (2D) structure: Glucose
Double-click on the Selection tool icon to invoke the Model Builder.
Choose <Semi-empirical> on the <Setup> menu.
Choose <PM3> and then L-click on <Options>. You can use any semi-empirical methods to compute UV-vis spectra.
In the Semi-empirical Options dialog box, choose RHF spin pairing, set Total charge, Spin multiplicity, and choose Lowest state.
You must use RHF spin pairing when you want to compute electronic spectra.
Choose CI.
Choose Singly Excited as the Cl Method. Singly Excited is the most efficient and well-defined way to calculate spectroscopic energies.
Choose Orbital Criterion, and specify the number of Occupied and Unoccupied orbitals. You can also use Energy Criterion.
The number of excited electronic states calculated is equal to the number of interacting configurations (determinants), which is given by the number of permutations of electrons going from occupied to unoccupied orbitals.
Close all open dialog boxes by L-clicking on the OK buttons, and then choose <Single Point> from the <Compute> menu.
HyperChem performs an SCF calculation to obtain the reference electronic configuration associated with the singlet ground state of the molecule. Next, HyperChem generates a series of singly excited configurations, computes the Hamiltonian matrix elements between them, and then diagonalizes the matrix to get the spectrum of electronic states.
When the calculation finishes, choose <Electronic Spectrum> on the <Compute> menu. Two sets of lines (transitions) appear in the dialog box. The top set shows all the excited electronic states (both singlet and triplet); the bottom set shows only states that are spectroscopically active and their relative intensities.
L-click on the right-most bottom line. This line changes to a violet line, indicating it is selected HyperChem displays information on this transition in the bottom of the dialog box.
VISUALISASI SIFAT MOLEKULER
Potential Energy Plots
Displays a potential energy surface. The independent variable depends upon the current selection status when you click on the menu item. If the current selection corresponds to an independent variable that variable is used for the plot. If the current selection does not correspond to an independent variable, then PLOT1 and PLOT2 are used for the independent variables. If none of these are appropriate, the menu item will be inactive (grayed).
PLOT1 and PLOT2 are the independent variables for a two-dimensional potential energy plot. Each of them must be a Named Selection. A two-atom named selection corresponding to a bond, or a three-atom named selection corresponding to a bond angle, or a four-atom named selection corresponding to a torsion are all appropriate independent variables. If you are requesting a one-dimensional potential energy plot, then either PLOT1 should be undefined or you should use the current selection to define the independent variable.
If the current selection corresponds to the atoms of a bond, an angle, or a torsion, then that structural moiety will be the independent variable and a one-dimensional potential energy plot will be suggested. If the current selection is the two atoms of a bond, then the first dialog box below will be requested. If the current selection is the three atoms of an angle or the four atoms of a torsion, then the second dialog box below will be requested.
If the current selection is not appropriate for the independent variable of a one-dimensional potential energy plot, then the Compute/Potential... menu item will enabled (un-grayed) only if PLOT1 and/or PLOT2 are defined. If at least PLOT1 is defined and the current selection is inappropriate for an independent variable, then the third dialog box below will be requested.
Procedure: Displaying a Potential Energy Surface (Compute Menu)
Displaying a One-Dimensional Potential
Select only the two atoms of a bond length, the three atoms of a bond angle, or the four atoms of a bond torsion.
L-click on <Compute> dan <Potential>.
Use the <Properties> button to modify the options used in the plot, if necessary
Displaying a Two-Dimensional Potential
Select only the two atoms of a bond length, the three atoms of a bond angle, or the four atoms of a bond torsion as the first independent variable.
L-click on <Select> dan <Name Selection> to name the selection as PLOT1.
Select only the two atoms of a bond length, the three atoms of a bond angle, or the four atoms of a bond torsion as the second independent variable.
L-click on <Select> dan <Name Selection> to name the selection as PLOT2.
L-click on <Compute> dan <Potential>.
Use the <Properties> button to modify the options used in the plot, if necessary.
Plot Molecular Properties: Molecular Properties Tab (Compute Menu)
Use this command if you want to display electrostatic potential, total spin density, or total charge density results of an semi-empirical or ab initio calculation. This command is unavailable unless a quantum-mechanical wavefunction has been calculated, via Single Point, Geometry Optimization, Molecular Dynamics, Langevin Dynamics, Monte Carlo, Vibrations, or Transition State.
Property:
 |
Representation:
 | |
 | |
 |
Procedure: Plot Molecular Graphs (Compute Menu)
Draw the 2D structure: NH3
Double-click on the Selection tool icon. HyperChem builds the molecule.
Choose <Semi-empirical> on the <Setup> menu.
Choose any of the Semi-empirical methods for a single point calculation.
Choose <Options>.
Set the <Total charge> and the <Spin multiplicity>, and then choose OK to close both dialog boxes.
Choose <Single Point> on the <Compute> menu.
When the calculation finishes, choose <Plot Molecular Graphs> on the <Compute> menu. The Plot Molecular Properties Options dialog box opens.
Select one of the properties : Electrostatic potential, Total spin density, Total charge density
Choose a representation. : 2D Contours, 3D Isosurface, 3D Mapped Isosurface
L-click on OK.
Orbital
The probability function describing the spatial distribution of an electron. Atomic orbitals describe the electrons in atoms. Molecular orbitals, derived as a linear combination of atomic orbitals (LCAO), describe electrons in molecules.
Once you have performed a semi-empirical or ab initio calculation you can choose Orbitals to display the contours of the energy levels for all orbits or an orbit you specify. Use the Orbits dialog box to see degeneracies and near degeneracies, HOMO-LUMO gaps, orbital occupation scheme, alpha and beta spin manifolds separately (for UHF calculations of open shell systems), d-d splittings (for transition metals).
Procedure: Orbitals (Compute Menu)
Draw the 2D structure: NH3
Double-click on the Selection tool icon. HyperChem builds the molecule.
Choose Semi-empirical on the Setup menu.
Choose any of the Semi-empirical methods for a single point calculation.
Choose Options.
Set the Total charge and the Spin multiplicity, and then choose OK to close both dialog boxes.
Choose Single Point on the Compute menu.
When the calculation finishes, choose Orbitals on the Compute menu. The Orbitals dialog box opens. The long dotted line in the middle of the dialog box represents zero energy. The violet lines represent virtual orbitals, and the green lines represent occupied orbitals.
L-click on the Labels option in the dialog box to see the filling of the orbitals.
Move the Orbitals dialog box to the side of the screen so you can see the HyperChem workspace.
Select an orbital.
The selected orbital level is highlighted in red. The values for the energy and the orbital designation appear in the Orbitals options box.
Choose 2D Contours or 3D lsosurface.
L-click on Plot.
Choose Number to number the orbitals starting from lowest energy orbital.
Choose HOMO to display the number of the orbital as an offset from the HOMO.
Choose LUMO+ to display the number of the orbital as an offset from the LUMO.
L-click drag a rectangle around a group of orbitals.
Choose Zoom to visualize the entire set of orbitals.
Contoh Hasil Perekam Komputasi Menggunakan <Start Log> dan <Stop Log>
HyperChem log start -- Sat Mar 29 09:03:41 2008.
Single Point, SemiEmpirical, molecule = D:\Documents and Settings\My Documents\diktat hyper\NH3.hin.
AM1
Convergence limit = 0.0100000 Iteration limit = 50
Accelerate convergence = NO
RHF Calculation:
Singlet state calculation
Number of electrons = 8
Number of Double Occupied Levels = 4
Charge on the System = 0
Total Orbitals = 7
Starting AM1 calculation with 7 orbitals
Iteration = 1 Difference = 1430.40403
Iteration = 2 Difference = 10.08501
Iteration = 3 Difference = 2.52484
Iteration = 4 Difference = 0.85492
Iteration = 5 Difference = 0.00598
Energy=-276.372055 kcal/mol Gradient=6.836424 Symmetry=C3V
ENERGIES AND GRADIENT
Total Energy = -5732.5124109 (kcal/mol)
Total Energy = -9.135338891 (a.u.)
Binding Energy = -276.3720549 (kcal/mol)
Isolated Atomic Energy = -5456.1403560 (kcal/mol)
Electronic Energy = -9987.6978735 (kcal/mol)
Core-Core Interaction = 4255.1854627 (kcal/mol)
Heat of Formation = -7.0660549 (kcal/mol)
Gradient = 6.8364239 (kcal/mol/Ang)
MOLECULAR POINT GROUP
C3V
EIGENVALUES(eV)
Symmetry: 1 A1 1 E 1 E 2 A1 3 A1
Eigenvalue: -32.426362 -15.814177 -15.814177 -10.371295 4.106811
Symmetry: 2 E 2 E
Eigenvalue: 6.111278 6.111278
ATOMIC ORBITAL ELECTRON POPULATIONS
AO: 1 S N 1 Px N 1 Py N 1 Pz N 2 S H
1.586398 1.203774 1.135901 1.475261 0.866222
AO: 3 S H 4 S H
0.866222 0.866222
NET CHARGES AND COORDINATES
Atom Z Charge Coordinates(Angstrom) Mass
x y z
1 7 -0.401334 -1.01432 0.15037 -0.04881 14.00700
2 1 0.133778 -1.01432 1.16037 -0.04881 1.00800
3 1 0.133778 -0.06208 -0.18629 -0.04881 1.00800
4 1 0.133778 -1.49043 -0.18629 0.77586 1.00800
ATOMIC GRADIENTS
Atom Z Gradients(kcal/mol/Angstrom)
x y z
1 7 -3.19825 -2.26151 -5.53947
2 1 -1.08454 12.91896 -1.87830
3 1 11.81867 -5.32866 -1.87838
4 1 -7.53588 -5.32879 9.29615
Dipole (Debyes) x y z Total
Point-Chg. 0.306 0.216 0.530 0.649
sp Hybrid 0.562 0.397 0.973 1.192
pd Hybrid 0.000 0.000 0.000 0.000
Sum 0.868 0.614 1.503 1.841
Geometry optimization, SemiEmpirical, molecule = D:\Documents and Settings\My Documents\diktat hyper\NH3.hin.
AM1
PolakRibiere optimizer
Convergence limit = 0.0100000 Iteration limit = 50
Accelerate convergence = NO
Optimization algorithm = Polak-Ribiere
Criterion of RMS gradient = 0.1000 kcal/(A mol) Maximum cycles = 60
RHF Calculation:
Singlet state calculation
Number of electrons = 8
Number of Double Occupied Levels = 4
Charge on the System = 0
Total Orbitals = 7
Starting AM1 calculation with 7 orbitals
E=-276.3721 kcal/mol Grad=0.000 Conv=NO(0 cycles 0 points) [Iter=1 Diff=1430.40403]
E=-276.3721 kcal/mol Grad=0.000 Conv=NO(0 cycles 0 points) [Iter=2 Diff=10.08501]
E=-276.3721 kcal/mol Grad=0.000 Conv=NO(0 cycles 0 points) [Iter=3 Diff=2.52484]
E=-276.3721 kcal/mol Grad=0.000 Conv=NO(0 cycles 0 points) [Iter=4 Diff=0.85492]
E=-276.3721 kcal/mol Grad=0.000 Conv=NO(0 cycles 0 points) [Iter=5 Diff=0.00598]
E=-276.3721 kcal/mol Grad=6.836 Conv=NO(0 cycles 1 points) [Iter=1 Diff=0.05705]
E=-276.3721 kcal/mol Grad=6.836 Conv=NO(0 cycles 1 points) [Iter=2 Diff=0.01105]
E=-276.3721 kcal/mol Grad=6.836 Conv=NO(0 cycles 1 points) [Iter=3 Diff=0.00332]
E=-276.6098 kcal/mol Grad=1.759 Conv=NO(0 cycles 2 points) [Iter=1 Diff=0.00075]
E=-276.6177 kcal/mol Grad=0.824 Conv=NO(1 cycles 3 points) [Iter=1 Diff=0.00206]
E=-276.6246 kcal/mol Grad=0.490 Conv=NO(1 cycles 4 points) [Iter=1 Diff=0.00269]
E=-276.6292 kcal/mol Grad=0.246 Conv=NO(1 cycles 5 points) [Iter=1 Diff=0.00917]
E=-276.6301 kcal/mol Grad=0.509 Conv=NO(1 cycles 6 points) [Iter=1 Diff=0.00014]
E=-276.6321 kcal/mol Grad=0.119 Conv=NO(2 cycles 7 points) [Iter=1 Diff=0.00020]
E=-276.6313 kcal/mol Grad=0.440 Conv=NO(2 cycles 8 points) [Iter=1 Diff=0.00008]
E=-276.6322 kcal/mol Grad=0.015 Conv=YES(3 cycles 9 points) [Iter=1 Diff=0.00000]
ENERGIES AND GRADIENT
Total Energy = -5732.7725376 (kcal/mol)
Total Energy = -9.135753429 (a.u.)
Binding Energy = -276.6321816 (kcal/mol)
Isolated Atomic Energy = -5456.1403560 (kcal/mol)
Electronic Energy = -10024.9418398 (kcal/mol)
Core-Core Interaction = 4292.1693022 (kcal/mol)
Heat of Formation = -7.3261816 (kcal/mol)
Gradient = 0.0227887 (kcal/mol/Ang)
MOLECULAR POINT GROUP
C3V
EIGENVALUES(eV)
Symmetry: 1 A1 1 E 1 E 2 A1 3 A1
Eigenvalue: -32.688079 -15.902410 -15.902410 -10.416908 4.223025
Symmetry: 2 E 2 E
Eigenvalue: 6.169775 6.169775
ATOMIC ORBITAL ELECTRON POPULATIONS
AO: 1 S N 1 Px N 1 Py N 1 Pz N 2 S H
1.580104 1.204235 1.136518 1.475097 0.868015
AO: 3 S H 4 S H
0.868015 0.868015
NET CHARGES AND COORDINATES
Atom Z Charge Coordinates(Angstrom) Mass
x y z
1 7 -0.395955 -1.01501 0.14988 -0.05000 14.00700
2 1 0.131985 -1.01182 1.14769 -0.04448 1.00800
3 1 0.131985 -0.07320 -0.17971 -0.04448 1.00800
4 1 0.131985 -1.48112 -0.17971 0.76839 1.00800
ATOMIC GRADIENTS
Atom Z Gradients(kcal/mol/Angstrom)
x y z
1 7 0.03193 0.02258 0.05531
2 1 -0.01167 -0.00172 -0.02021
3 1 -0.00551 -0.01043 -0.02021
4 1 -0.01475 -0.01043 -0.01488
Dipole (Debyes) x y z Total
Point-Chg. 0.304 0.215 0.526 0.644
sp Hybrid 0.567 0.401 0.981 1.202
pd Hybrid 0.000 0.000 0.000 0.000
Sum 0.870 0.615 1.507 1.846
Vibrational Analysis, SemiEmpirical, molecule = D:\Documents and Settings\My Documents\diktat hyper\NH3.hin.
AM1
Convergence limit = 0.0100000 Iteration limit = 50
Accelerate convergence = NO
RHF Calculation:
Singlet state calculation
Number of electrons = 8
Number of Double Occupied Levels = 4
Charge on the System = 0
Total Orbitals = 7
Starting AM1 calculation with 7 orbitals
Iteration = 1 Difference = 1444.16939
Iteration = 2 Difference = 9.92973
Iteration = 3 Difference = 2.55998
Iteration = 4 Difference = 0.87677
Iteration = 5 Difference = 0.00571
ENERGIES AND GRADIENT
Total Energy = -5732.7716372 (kcal/mol)
Total Energy = -9.135751994 (a.u.)
Binding Energy = -276.6312812 (kcal/mol)
Isolated Atomic Energy = -5456.1403560 (kcal/mol)
Electronic Energy = -10024.9409395 (kcal/mol)
Core-Core Interaction = 4292.1693022 (kcal/mol)
Heat of Formation = -7.3252812 (kcal/mol)
Gradient = 0.2339703 (kcal/mol/Ang)
MOLECULAR POINT GROUP
C3V
EIGENVALUES(eV)
Symmetry: 1 A1 1 E 1 E 2 A1 3 A1
Eigenvalue: -32.690167 -15.904118 -15.904118 -10.417706 4.220990
Symmetry: 2 E 2 E
Eigenvalue: 6.166559 6.166559
ATOMIC ORBITAL ELECTRON POPULATIONS
AO: 1 S N 1 Px N 1 Py N 1 Pz N 2 S H
1.580769 1.203917 1.136369 1.474102 0.868281
AO: 3 S H 4 S H
0.868281 0.868281
NET CHARGES AND COORDINATES
Atom Z Charge Coordinates(Angstrom) Mass
x y z
1 7 -0.395158 -1.01501 0.14988 -0.05000 14.00700
2 1 0.131719 -1.01182 1.14769 -0.04448 1.00800
3 1 0.131719 -0.07320 -0.17971 -0.04448 1.00800
4 1 0.131719 -1.48112 -0.17971 0.76839 1.00800
ATOMIC GRADIENTS
Atom Z Gradients(kcal/mol/Angstrom)
x y z
1 7 0.33071 0.23385 0.57280
2 1 -0.11271 -0.09145 -0.18399
3 1 -0.12055 -0.06661 -0.18960
4 1 -0.09745 -0.07578 -0.19920
Dipole (Debyes) x y z Total
Point-Chg. 0.303 0.214 0.525 0.643
sp Hybrid 0.567 0.401 0.983 1.204
pd Hybrid 0.000 0.000 0.000 0.000
Sum 0.870 0.616 1.508 1.846
**********************************
****** Vibrational Analysis ******
**********************************
Computing the force matrix: done 20%.
Computing the force matrix: done 50%.
Computing the force matrix: done 70%.
Computing the force matrix: done 100%.
Calculating the vibrational spectrum...
==== Force Constant Matrix in Milli-Dynes / Angstrom ====
(I -- Atom Index Z Atomic Number)
I Z I Z I Z I Z I Z
1 7 2 1 3 1 4 1
1 7 6.95041 3.09898 3.09891 3.09878
2 1 3.09898 3.44291 0.42670 0.42670
3 1 3.09891 0.42670 3.44283 0.42671
4 1 3.09878 0.42670 0.42671 3.44274
==== Zero Point Energy of Vibration in kcal / mol ====
21.60589
=================================
========== IR Spectrum ==========
=================================
---- Normal Mode Frequencies of Vibration in 1/cm.
---- Integrated Infrared Band Intensities in km/mol.
---- Derivatives of Dipole Moments with Respect
to Normal Coordinates in Debye/Angstrom/AMU.
*****************************************************************************
Normal Mode Frequency 1139.20
1 Intensity 37.47432
Symmetry 1 A1
Derivatives of Dipole Moment -0.6736 -0.4763 -1.1667
Normal Mode Frequency 1764.71
2 Intensity 0.00003
Symmetry 1 E
Derivatives of Dipole Moment 0.0001 -0.0012 0.0004
Normal Mode Frequency 1764.72
3 Intensity 0.00003
Symmetry 1 E
Derivatives of Dipole Moment 0.0011 0.0000 -0.0005
Normal Mode Frequency 3465.08
4 Intensity 2.71713
Symmetry 2 E
Derivatives of Dipole Moment 0.2970 0.1120 -0.2174
Normal Mode Frequency 3465.12
5 Intensity 2.71566
Symmetry 2 E
Derivatives of Dipole Moment -0.1639 0.3449 -0.0463
Normal Mode Frequency 3535.03
6 Intensity 1.94860
Symmetry 2 A1
Derivatives of Dipole Moment 0.1536 0.1087 0.2660
Translation Frequency 0.00
1 Intensity 0.00000
Derivatives of Dipole Moment 0.0000 0.0000 -0.0000
Translation Frequency -0.00
2 Intensity 0.00000
Derivatives of Dipole Moment -0.0000 0.0000 -0.0000
Translation Frequency 0.00
3 Intensity 0.00000
Derivatives of Dipole Moment 0.0000 0.0000 -0.0000
Rotation Frequency -14.16
1 Intensity 38.67454
Derivatives of Dipole Moment -0.8381 1.1852 0.0000
Rotation Frequency -16.46
2 Intensity 38.67251
Derivatives of Dipole Moment -0.9677 -0.6843 0.8381
Rotation Frequency 10.30
3 Intensity 0.00000
Derivatives of Dipole Moment -0.0000 0.0000 -0.0000
*****************************************************************************
Transition State Search: Eigenvector Following, SemiEmpirical, molecule = D:\Documents and Settings\My Documents\diktat hyper\NH3.hin.
AM1
Convergence limit = 0.0100000 Iteration limit = 50
Accelerate convergence = NO
RHF Calculation:
Singlet state calculation
Number of electrons = 8
Number of Double Occupied Levels = 4
Charge on the System = 0
Total Orbitals = 7
Starting AM1 calculation with 7 orbitals
Computing the Hessian is required.
Computing the Hessian using Cartesian coordinates.
Iteration = 1 Difference = 1444.16939
Iteration = 2 Difference = 9.92973
Iteration = 3 Difference = 2.55998
Iteration = 4 Difference = 0.87677
Iteration = 5 Difference = 0.00571
Computing the initial Hessian: done 20%.
Computing the initial Hessian: done 50%.
Computing the initial Hessian: done 70%.
Computing the initial Hessian: done 100%.
ENERGIES AND GRADIENT
Total Energy = -5732.7723775 (kcal/mol)
Total Energy = -9.135753174 (a.u.)
Binding Energy = -276.6320215 (kcal/mol)
Isolated Atomic Energy = -5456.1403560 (kcal/mol)
Electronic Energy = -10024.9416797 (kcal/mol)
Core-Core Interaction = 4292.1693022 (kcal/mol)
Heat of Formation = -7.3260215 (kcal/mol)
Gradient = 0.0941420 (kcal/mol/Ang)
MOLECULAR POINT GROUP
C3V
EIGENVALUES(eV)
Symmetry: 1 A1 1 E 1 E 2 A1 3 A1
Eigenvalue: -32.688693 -15.903097 -15.902680 -10.417151 4.222420
Symmetry: 2 E 2 E
Eigenvalue: 6.168701 6.168895
ATOMIC ORBITAL ELECTRON POPULATIONS
AO: 1 S N 1 Px N 1 Py N 1 Pz N 2 S H
1.580323 1.204297 1.136524 1.474563 0.868094
AO: 3 S H 4 S H
0.868094 0.868105
NET CHARGES AND COORDINATES
Atom Z Charge Coordinates(Angstrom) Mass
x y z
1 7 -0.395707 -1.01501 0.14988 -0.05000 14.00700
2 1 0.131906 -1.01182 1.14769 -0.04448 1.00800
3 1 0.131906 -0.07320 -0.17971 -0.04448 1.00800
4 1 0.131895 -1.48112 -0.17971 0.76839 1.00800
ATOMIC GRADIENTS
Atom Z Gradients(kcal/mol/Angstrom)
x y z
1 7 0.15018 0.10618 0.20023
2 1 -0.03515 -0.02380 -0.03607
3 1 -0.03414 -0.02518 -0.03603
4 1 -0.08089 -0.05719 -0.12813
Dipole (Debyes) x y z Total
Point-Chg. 0.303 0.215 0.525 0.644
sp Hybrid 0.567 0.401 0.982 1.203
pd Hybrid 0.000 0.000 0.000 0.000
Sum 0.871 0.616 1.507 1.846
**************************************************************************************
HyperChem log stop -- Sat Mar 29 09:04:26 2008.
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