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TUTORIAL HYPERCHEM

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 Energi keadaan tereksitasi CI


isomer
Sifat dan struktur keadaan
Panas pembentukan transisi
Energi aktivasi Energi interaksi non-bonded

Muatan atom Spektra serapan UV-VIS

Beda energi HOMO-LUMO Spektra Absorpsi IR

Potensial Ionisasi Pengaruh isotop pada vibrasi

Afinitas elektron Spektra serapan IR

Momen dipol Efek Collision pada sifat


struktur
Tingkat energi elektronik
Stabilitas dari kluster
Energi korelasi elektron MP2

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:

: button `Drawing' untuk menampakkan sistem periodik unsur; cara melakukanya

: button `Selection' untuk memilih atom atau molekul atau untuk melihat panjang
ikatan, sudut ikatan, dan sudut torsi

: button `XY Rotation' untuk memutar molekul sekitar sumbu X dan Y

: button `Z Rotation' untuk memutar molekul sekitar sumbu Z

: 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

: 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>

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
Bagaimana membuatetena(CH2CH2) yang ordeikatannya 2 ?

1. Lakukan langkah (1) sampai(5) seperti di atas, persis!

2. Klik button toolbars[Draw] 1 kali,laluarahkan kursor bertanda<select>dan


tempatkantepatpada garisikatan,klik kiri mouse 1 kali saja,maka akan muncul ikatan
ganda.
Untuk membuatetuna(CHCH) yang berorde ikatan 3, maka lakukanklik seperti ini2kali
klikkiri mouse,sehingga muncul ikatan tripel.

3. Baru lalukan langkah (6) dan (7).


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 [ z o o m ]

MELIHAT PANJANG IKATAN, SUDUT IKATAN, DAN SUDUT TORSION

Klik <Select> dan pilihlah <Atoms>, untuk memilih atom-atom

Klik button toolbars [Select] 1 kali saja

Untuk 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>

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

MEMBUAT STRUKTUR MOLEKUL DART CS CHEMDRAW ULTRA

Aktifkan program CS ChemDraw Ultra

Klik button tool text 1 kali

Misal akan membuat struktur TNT (Trinitrotoluene), klik kiri mouse di ruang kosong,
kemudian ketik `trinitrotoluene' (harus istilah asing)

Klik button tool Marquee 1 kali saja

Klik 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),

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 and 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 HyperChem

Creating a Sample Crystal

L-click on Databases/Crystals to bring up the Crystal Builder Module

L-click on the Samples...... button

Select an appropriate Sample Crystal Type and then L-click on OK

Select the Number of Unit Cells in the Crystal Builder Module

L-click on HyperChem/Put in the Crystal Builder Module

Close the Crystal Builder Module by an L-click in the upper right-hand corner.

Return to HyperChem
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
Schrdinger. 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 Schrdinger 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 Schrdinger 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.


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 Schrdinger 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 am a 5 i a a 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 atoms 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 1E 1E 2 A1 3 A1

Eigenvalue: -32.426362 -15.814177 -15.814177 -10.371295 4.106811

Symmetry: 2E 2E

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 1E 1E 2 A1 3 A1

Eigenvalue: -32.688079 -15.902410 -15.902410 -10.416908 4.223025

Symmetry: 2E 2E

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 1E 1E 2 A1 3 A1

Eigenvalue: -32.690167 -15.904118 -15.904118 -10.417706 4.220990

Symmetry: 2E 2E

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 1E

Derivatives of Dipole Moment 0.0001 -0.0012 0.0004

Normal Mode Frequency 1764.72

3 Intensity 0.00003

Symmetry 1E

Derivatives of Dipole Moment 0.0011 0.0000 -0.0005

Normal Mode Frequency 3465.08

4 Intensity 2.71713

Symmetry 2E
Derivatives of Dipole Moment 0.2970 0.1120 -0.2174

Normal Mode Frequency 3465.12

5 Intensity 2.71566

Symmetry 2E

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 1E 1E 2 A1 3 A1

Eigenvalue: -32.688693 -15.903097 -15.902680 -10.417151 4.222420

Symmetry: 2E 2E

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.