tutorial hyperchem 2

TUTORIAL HYPERCHEM

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

Dengan klik 2 kali secara cepat

: 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 membuat etena (CH2CH2) yang orde ikatannya 2 ?

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

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

tempatkan tepat pada garis ikatan, klik kiri mouse 1 kali saja, maka akan muncul

ikatan ganda.

Untuk membuat etuna (CHCH) yang berorde ikatan 3, maka lakukan klik seperti

ini 2 kali klik kiri 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 [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

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

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.

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), topredict

electronic properties of molecular systems. Ab initio calculations use different

approximations to the Schrodinger equation, without empirical parameters.

Semi-empirical

Atype 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 pointconfiguration 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);





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.



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


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


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.



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 <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


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.


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



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


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





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



Optimization algorithm = Polak-Ribiere

Criterion of RMS gradient = 0.1000 kcal/(A mol) Maximum cycles = 60

RHF Calculation:





Total Orbitals = 7


E=-276.3721 kcal/mol Grad=0.000 Conv=NO(0 cycles 0 points) [Iter=1

Diff=1430.40403]


Diff=10.08501]


Diff=2.52484]


Diff=0.85492]


Diff=0.00598]


Diff=0.05705]


Diff=0.01105]


Diff=0.00332]


Diff=0.00075]


Diff=0.00206]


Diff=0.00269]


Diff=0.00917]


Diff=0.00014]


Diff=0.00020]


Diff=0.00008]

E=-276.6322 kcal/mol Grad=0.015 Conv=YES(3 cycles 9 points) [Iter=1

Diff=0.00000]



Total Energy = -9.135753429 (a.u.)








C3V

EIGENVALUES(eV)


Eigenvalue: -32.688079 -15.902410 -15.902410 -10.416908 4.223025

Symmetry: 2 E 2 E

Eigenvalue: 6.169775 6.169775



1.580104 1.204235 1.136518 1.475097 0.868015

AO: 3 S H 4 S H

0.868015 0.868015



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


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


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



RHF Calculation:





Total Orbitals = 7









Total Energy = -9.135751994 (a.u.)








C3V

EIGENVALUES(eV)


Eigenvalue: -32.690167 -15.904118 -15.904118 -10.417706 4.220990

Symmetry: 2 E 2 E

Eigenvalue: 6.166559 6.166559



1.580769 1.203917 1.136369 1.474102 0.868281

AO: 3 S H 4 S H

0.868281 0.868281



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


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


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%.




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


2 Intensity 0.00003

Symmetry 1 E

Derivatives of Dipole Moment 0.0001 -0.0012 0.0004


3 Intensity 0.00003

Symmetry 1 E

Derivatives of Dipole Moment 0.0011 0.0000 -0.0005


4 Intensity 2.71713

Symmetry 2 E



5 Intensity 2.71566

Symmetry 2 E

Derivatives of Dipole Moment -0.1639 0.3449 -0.0463


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


Translation Frequency -0.00

2 Intensity 0.00000


Translation Frequency 0.00

3 Intensity 0.00000


Rotation Frequency -14.16


Derivatives of Dipole Moment -0.8381 1.1852 0.0000

Rotation Frequency -16.46


Derivatives of Dipole Moment -0.9677 -0.6843 0.8381

Rotation Frequency 10.30

3 Intensity 0.00000


*****************************************************************

************

Transition State Search: Eigenvector Following, SemiEmpirical, molecule =

D:\Documents and Settings\My Documents\diktat hyper\NH3.hin.

AM1



RHF Calculation:





Total Orbitals = 7


Computing the Hessian is required.

Computing the Hessian using Cartesian coordinates.






Computing the initial Hessian: done 20%.






Total Energy = -9.135753174 (a.u.)








C3V

EIGENVALUES(eV)


Eigenvalue: -32.688693 -15.903097 -15.902680 -10.417151 4.222420

Symmetry: 2 E 2 E

Eigenvalue: 6.168701 6.168895



1.580323 1.204297 1.136524 1.474563 0.868094

AO: 3 S H 4 S H

0.868094 0.868105



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


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


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.

H